There is gap below my application menu bar so i tried toggling it the compositor(shift+alt+f12) it fixes that but then my latte dock turns full opaque (which I usually keep slightly less opaque) with no animations working and also i am unable to configure the background of latte dock. But on toggling compositor again, latte dock will turn back normal but unfortunately the gap will come again.

Now I removed latte dock but no good still I have to toggle the compositor to remove the gap on every restart.

Transparency requires compositing, so there's that.
Screenshots of the gap would be appreciated.
Also you might try different plasma themes as I suspect it may depend on which theme you are using.