Hi
Problem with the save method is known…
And to have everyone happy I think there’s no real solution except trying to implement options that allows user to determinate how the save dialog will work (like now, like Gimp, like…)
Currently, I’m using another method through plugin BuliCommander - #17 by Grum999.
Rather than having problem with saving non Kra file, open non kra file as Krita document:
Then, when saving, the (opened jpeg or png file) is already converted to Krita document and there’s no problem 
Currently when opened as new document, there’s no name and I may add an option to keep original file name (something like test.png might be automatically named as test.kra or test.png.kra)
Grum999