I'm no computer programmer BUT I would think implementing a "Reset Measure/Bar Number" should be fairly simple. Adobe Audition has it:
This affects only the Measure numbers of the Time Ruler. Actual SMPTE/Broadcast Wave time stamps remain in the realm of "Absolute" time regardless of what is perceived as measure 1:01:000.
Having said that, notation programs will still see the "count-in" measures [I
do believe that the implementation of some sort of "offset" function for SMPTE time stamps to account for the "count-in" measures would either be asking for trouble or a major coding issue...Just my opinion because, as I said, I'm no computer programmer].
Anyway, the "workaround" I sometimes use when getting ready to prepare a score (or print individual parts in Sibelius) is to
"Save As" a copy of the project as a MIDI file in the
"Score" sub-folder of the project's parent folder (or individual MIDI files depending on what I'm actually working on) and simply slide everything over to the approriate starting point so that Measure "1" is actually the beginning of the song--If there are "pickup notes" leading into a "downbeat of the first full measure they are STILL a part of Measure "1", the measure just includes some "rests" before the song begins with the pickup notes. Yes, it's an "extra" step but it's a relatively minor issue to deal with when I'm truly concerned with accurate measure/bar numbers.
Just my 2¢ worth.