Your rationale would only make sense if only robots would use paint.net which isn't the case. Usually people press ctrl+s reflexively, in which case you end up overwriting a lossy file unrecovaribly. At least with lossy files you can recover the original, by undoing everything and saving it. The inability to undo a step with an image editor sucks a lot.
If the user could specify a default save format, it would prevent such unexpected things from happening, but that's not possible either as far as I can tell.
I'm aware of that. Yet if you press ctrl+s there's no going back, no matter if you decide to "save as" after. Well, the quality prompt helps a bit. (Not sure if it appeared for edited jpg-s when I reported this)