BBEdit not the same on the app store?

There’s an update to BBEdit today, in which they list the following in their fixes/notes (emphasis added):

If “Make Writeable” fails because you have insufficient (non-elevated) privileges, BBEdit will flag the file for authenticated saving instead of refusing to let you do anything. (Note: This does not apply to App Store versions of BBEdit, which are not able to perform authenticated saves.)

I’ll admit I haven’t paid a lot of attention to the App Store yet, but this concerns me. Are there functionality differences between what the App Store will allow and what might be possible outside of it? If so, that’s a problem.