IMHO, if Aces High modeled high-altitude level bombing such that accuracy declined as altitude increased (as in real life), then this would be less of an issue.
Drediock, as for what constitutes "historical" bombing altitudes, just a small selection from the 303rd Bomb Group web site which you cited shows the following:
mission # 356
Bombing Altitudes: 24,000, 23,800 & 24,600 feet
mission # 357
Bombing Altitudes: 25,000, 24,000& 26,000 feet
mission #358
Bombing Altitudes: 26,500, 26,000 & 27,500 feet