I've tested the app on Linux Mint 20.03 with i3 wm and I could not reproduce the issue.
The things you're saying about your file's geometry being malformed are disturbing yes, but I can't determine the reason behind such behavior.
I've rechecked the code and image geometry is set only during the loading process directly from image file, there's no any 'calculation' step involved (aside from possible PNG loading code inside Qt).
Also, changing the grid size does not affect atlas or image dimensions.
Existing atlases loader seems to be doing fine too.
I'm sorry to hear about your troubles, but so far I could only theorize that your image somehow became "incompatible", which caused a glitch within PNG loader, but this is just another wild guess - I've tested the app with many PNGs from various sources (pinterest, twitter, Adobe Photoshop, GIMP, Krita, Aseprite). Or the issue could be caused by an unlikely bug inside Qt loader (has nothing to do with your system version).
If this issue will occur again, I suggest working around by editing atlas' JSON file - it's fields "width" and "height", as inconvenient as it is.
Or we could pursue 100% reproduction angle with detailed repro-steps. If you manage to find out how to make this issue appear consistently, it would be much appreciated, because then I will be able to fix it.
Thanks.