I wonder how do you deal with transparent TGA files inside Krita, is it doable? I have some textures from the 3d app I'd like to edit with Krita, but the transparent opens (and saves) as black (2.9.9).

Hum, 2.9.9 had a fix for tga import/export that dealt with transparency. This fixed the issue for tga's saved from gimp, but it might have broken your tga's.

I'll reopen https://bugs.kde.org/show_bug.cgi?id=354791, could you attach a sample file to that bug?

Archive with sample file added to the bug report.