Thanks for this topic creation 
As I already said here (Deleted texture leaves imprint on sheer layer - #13 by Grum999), the way GIMP works doesn’t allows user to save a file with another file format than .xcf from Save & Save As dialog box; user must use the Export function to save a file as .png or .jpeg for example.
This can make sense as using another file format than native file format doesn’t allow to save all layers and other information, and it could be a source of frustration when you realize that you’ll lost most of your work and only have a single merged picture as result.
But, on my side I always been bored by the fact I have to Export rather than Save.
Don’t know why, but it’s not natural for me even if it make sense 
Yes, but for a beginner:
- Kra file format is something unknown and looking on the forum, you can see that some people use .png or .jpeg instead of .kra to save their work because they know these extensions and don’t understand what .kra is and means
- By opening a .png file to start to work on it, by default it will propose you to save as .png and then, if you have layers they’ll be lost
Yes, but by experience, people don’t read messages from dialog box… you don’t imagine what I already saw at the office 
So maybe, an option in Configure Krita > General > File handling could be the best compromise:
(*) Save file dialog only allow to save native Kra file (like GIMP, default option for new installation)
( ) Save file dialog allows to save to any file format only if compatible (a compromise, default option for updated installation)
( ) Save file dialog allows to save to any file format (like now, with warning on file dialog)
Grum999