Certainly we know the stardates used in the TNG era can't be reconciled with TOS stardates, since if they go up 1000 units per year and 41000 is the start of 2364, then the whole thing would've only begun in 2323.
This isn't really a problem, because we are forced to assume the existence of "dropped digits" in any case, for both systems. Starfleet cannot be so blind to history that it would operate on a system that is only good for dealing with one decade at most (TOS) or one century at most (TNG), especially with the zero point more than a century into the existence of the organization - but if the system has, say, six digits, then 2323 simply means the year when the century digit last rolled.
If 2363/64 is in the 41XXX range, then the TOS episodes in the putative "previous" 41XXX range would fall on 2263/64, which isn't too problematic a concept. OTOH, since the five-year mission ended in 2270, the last TOS date would have to be in the "previous" 48XXX range, and the first episode qualifying as being part of the five-year mission would be "The Menagerie" at SD 3012... Unless Kirk just spent two years returning from his five-year mission.