Just to be clear: I don't think I have ever been asked (via a popup message) whether I want to save an edited file in a version set. Are you seeing something different than me? If so, please provide a screenshot and describe your workflow in more detail. The option to save a file in a version set is found in the Save As dialog. If you uncheck the box, the file will simply be saved with a new name and will appear alone in the Media grid (if you have also chosen to Include the file in the Organizer.) Once you have made your choices in the Save As dialog, they remain sticky and will apply to all future edits until you change the choice(s).
The Save File preference mentioned by @MichelBParis provides several different choices too. If you like to live dangerously and don't care whether you accidentally delete the original of an image that you have edited, then by all means change your options there.