A portable version is a version that could be write files on the system, but a very good portable version is one that full isolated from the system!
Full isolated means, the version doesn't write in other folders on the system as it's own folder!

Right now Krita is not full isolated because on windows systems it's writing in %localappdata% (AppData/Local) and this is bad, very bad!

This next portable version should be a full isolated one please!

You think it's so very, very bad? Well, why don't you fix it.

I don't think it's important, but patches are welcome.

It stores various data in there which can be shared across different krita builds on your system so that you don't have to set it up all over again for every updates and switches. There are tons of other softwares that use the same method. It's no good or bad, it just how it works.

If you're concerned about overwriting or 'contaminating' existing settings, that's what backup copies are for. I always have a recent backup copy of my krita config files and krita resources folder, in case I get careless or go too experimental with it.

If you want 'portability', that's what USB memory sticks are for. You can port your krita config files and krita resources folder over to another PC and then have krita look and feel and behave exactly as it did on the original PC.

InDiePix might find my post useful: Re: Where are settings stored in "portable" (!) version?