Well, if we were talking about different KINDS of minor scales, there would be
a difference then. For example, C mel minor only has 1 flat, which would be E flat.
C harm minor has 2 flats. Neither of these have the same key signature as Eb major.
Their scale tone intervals are different than the major key.

The melodic minor scale has three whole tone intervals spaced together, which you won't find in the major scales. Likewise, the harmonic minor scale has a minor third "skip" caused by raising the 7th tone a half step.

BIAB only allows us to use the major keys, and the equivalent (also called) natural minor key, which is simply a minor third transposition of a major scale.
Example: A minor is the same as the C major scale.

I don't have a problem with using the enharmonic mode, but the errors are much more extensive. The PITCHES are wrong, so it means a complete re-edit of the entire melody. And of course, you might have read about the unwanted extra notes.

If you have to do all that, it's less trouble to start over. Maybe put the melody into Finale, then import the MIDI file.

Wm. S. Sinclair