Some keybinds could be more intuitive, others could just exist... For convenient formatting, I highlighted the functions I am talking about with bold letters and underlined the keybinds I am suggesting for them.

The first one I would have recommended was Ctrl + R to reset canvas transformations, but seems in the git build this was already done it was the most important one too. Notice however that this keybind is also on "Rectangular Selection Tool" as such Rectangular Selection Tool needs a new bind. (I suggest one below, it's R, just R.)

Notice that there are two entries in the keybind menu for "Deselect"

But I would like to suggest since Ctrl+D is currently not in use by anything as default to add it as an alternative keybind for Deselect. This is the default button for many other programs to deselect and it couldn't hurt to do this, could it? Deselect is a very much used function and as such it is ideal that you don't have to cramp up your hand to use it, ctrl+shift+a (or ctrl+shift+anything) is kinda unintuitive. Ctrl+Shift should be a last resort kind of thing in my opinion.

Rectangular Selection Tool to R, since it cannot share it's binds with Reset Rotation.

Full Screen Mode could be Ctrl + F instead of Ctrl + Shift + F (Yes, because it can! it's easier and Ctrl+F is unbound!)

Close (Ctrl+W/Ctrl+Esc) should be UNBOUND, it's a dangerous **** and it already lost me my work once there's no need to have "close" bound in a painting application and it is more dangerous thani useful. It might not be so bad to use the then freed up CTRL+W bind for "Remove Layer" which is an undoable mistake if it were to occur, and a potentially useful button as well when intentionally used.

Increase/Decrease opacity should be bound to Shift + A and Shift + S

Darker/Lighter color should also be Shift + Q and Shift + W

My reasoning for the above two is that the ideal placement of important keyboard shortcuts should always be to the left of the 5/T/G/N line. Within easy reach of the left hand in its most natural position on a keyboard for anyone who used keyboard for a long time. (The reason B and V are within range is because of the thumb )

Show grid should be Ctrl + G

Transform Layer from Ctrl+T to Shift+T (It is significantly easier to press shift+T, at least as an alternative binding)

Outline Selection tool to S (Currently Unbound)

Crop Tool to Z (because we can)

Painter's Tools to A (as in pressing A should pop up the painter's tools menu near the cursor (within the boundaries of the screen though) because it is an awesome menu)

That's about it for now. I didn't go very thoroughly through this whole thing because to be hones the Keyboard Shortcut configuration menu looks a bit duct-taped together so it's not very pleasant to browse through it.

But if any developer is up for it, the way I would approach revising the keybinds is to look first for everything that is bound to CTRL+SHIFT or CTRL+ALT and consider: "Is that really necessary?"
Unless it's a global keybind (like ctrl+shift+z, which is the global bind for redo) it is not necessary and therefore should be simplified to either Ctrl Shift or Alt, only one of them, not all.

Which one should just be up to the programmer (ideally what feels most comfortable and feels like it makes most sense each time)

After this, I'd sniff up any keybinds that are anywhere on the right from 5, T and G (not N, it's easy to find buttons on the lowest line on the keyboard so M, ,, . and / make sense) and check if you can't find a better place for them within reach of ctrl/shift or alt with just one hand without stretching it.

Normally people should have one hand on the keyboard and one on the tablet when drawing, and if they can't just "feel" the buttons they need to press, they're going to lose focus which is going to happen if they need to press many buttons at once (3 buttons is many) or if it is outside of the comfort zone of their left hand which I just identified as anything right of 5TGN (that is 4RFVB are a comfortable stretch for pretty much everyone, people with short fingers need to stretch for 5TGN and 6YH is out of reach for everyone, but M can work out because it's easy to find due to its alignment with the spacebar)

Keybinding well is a bit of an art in itself. Remember when all the video games used the arrow keys? how were you supposed to use a mouse with that? If it's not within comfortable reach of the left hand that is normally on the keyboard, then you will have to look at the keyboard to find the button (or get like a 65% chance of hitting the wrong button)

And what about left-handed people? As in, those that draw with left? Or do I have to bind all common functions to the tool-bar(which is how I get around the ctrl+z problem, the straight-line tool however is already a night-mare, and I don't even touch anything further than V).

On top of that, realise that the shortcut saving is broken right now(it's not an easy fix, as there have been many attempts at fixing it).

Hey now, one of my favorite artists and biggest inspirations is left handed. Left handed people should already be used to keybindings being catered towards right handed people even if I totally agree with you that it is wrong, and would gladly assist in fixing it if it were within my power. But I'm not Logitech or any other major peripheral manufacturer. A theory worth looking into however if a program can be developed to re-arrange the order of the keys on a keyboard in Linux. It's a feasible idea, the tools to do it are already here.

I think that programs should always provide two presets for keybindings, one for right handed and one for left handed people.

Left handed keyboards seem like theres not enough of them developed to be viable for use or standardization, I haven't seen a left handed gamer keyboard nor a standardized keyboard built around using your right hand on it. My best friend is left handed but he uses the keyboard and mouse the same way as right handed people (it's easier to train than you'd think, drawing is sadly a bit more complex than moving a mouse), I once had my right arm knocked into an unusable state for two weeks, throughout that period I used the mouse on the left side and it felt a bit funky, but not bad. I have another friend who is right handed and actually prefers to have the mouse in his left hand and keyboard on the right hand wonder how he came down to that.

The keybinds are already bad for both left handed and right handed people. These changes would just make them less bad for right handed people.

Naturally yes, left handed people right now and after minor changes like I just suggested would need to rebind the entire selection of keys one way or another. The real problem with standardizing a layout for left handed people is that the symbols next to 0/P/L/M vary greatly between country of origin for the keyboard. For me next to L there is Æ. And then next to that is +. Next to P I have Ð. Whereas on the left side it's the usual QWERTY. This is the difficult side of the keyboard

But if I'd work on it I could probably come up with a solution for a preset catered towards the left handed, naturally being left handed means that you're going to have your hand around the ctrl/shift/enter/backspace/altgr/meta keys unless you have one of those specialized left handed keyboards which like I said are rare and don't seem to have any standardized form factor. (silliness though, how complicated could it be to just reverse the order of the keys like they are now? numpad and arrow keys on the right side, ctrl/alt/shift/qwer on the right side, I'm curious why this isn't a standard yet)

For now for left handed people, the viable range of buttons would have to be something like 8/U/H/V (this means that 9/I/J/N is the comfortable range, 8/U/H/V is a maximum stretch). But unfortunately this side of the keyboard is kind of mangled and unwieldy when you need to press CTRL. since it is a whole button further from the hand than it is in the normal right handed setup, but it's at least a sort of starting point. If you do your own keybinds you will probably have to sacrifice the sensibility of button names in context with the function they are bound to (for example there's no "R for rectangle anymore, that's out of reach)

If the keyboard shortcut saving and profile systems get fixed and start to function properly for once, I would be willing to help set up a sensible (or as sensible as possible) left handed keybind preset. It would be comfortable but since theres no standard, it doesn't matter what I would come up with it would always take people time to get used to.

There simply isn't any standard for left handed people yet, but it is needed, I agree with you. Maybe I can figure out a way to use the primary and alternative keybinds to set things up in a fashion that is convenient for both, but this would take quite a bit of work that I can't do right now. Moreover, if I would there's no guarantee the developers would accept these changes if I would go dive into the code and adjust the default keybinds myself, so it could just be wasted effort if I do.