Well, I don't know about that. I think the intent was to mimick USN aircraft numeration, like Dave suggested. Like we've been lead to believe, DYRL? is supposed to reflect the accurate look of the SDF Macross universe, and numbers on the VF-1s were sequential (at least to some extent).
I imagine that there is a certain set of numbers used for either a carrier air group or a squadron and repeated in various other CAGs or squadrons. It wouldn't be too hard to discern Skull 001 from say, Longhorn 001 at a glance (assuming there are certain squadron markings being used, either low-vis or otherwise), so the fact that they might share the same ID number wouldn't be much of an issue, even while assigned to the same carrier.
As for the "1023" on the VF-1D, if it wasn't an error, one might guess that 1023 is part of the aircraft's entire BuNo and the 102 was derived from it.