Yeah. While the TOS numbers were intended to be nonsensical, they were also apparently mostly intended to be systematic, with smaller ones indicating earlier dates. In the few cases where the ordering of SD numbers differs from the ordering of production dates, the plotlines actually make more sense if we follow the stardates (say, "Catspaw" coming before "Space Seed" and thus Chekov being aboard to meet Khan), although this is completely unintentional.
But as said, we can go one level further in "makes unintentional sense" here. By choosing to treat TOS stardates exactly like TNG era ones, we witness five years passing between Kirk's first TOS appearance and his last, not mere three. Overall, assuming that a thousand stardates equate one calendar year is a good match for what we see in TOS - up to and including the idea that the three zeroes roll at the beginning of each shooting season, at the end of the summer, rather than at January 1st (say, Thanksgiving in "Charlie X" falling in the middle of the first stardate year).
Of course, any system that can only list years and not decades is impractical for longterm timekeeping. With four digits, the TOS system would have to roll over every ten years; with five digits, the TNG one would have to do that every century. But we can assume Starfleet drops digits much like we do: if I say "Back in sixty-nine", it's understood I refer to 1969 unless the context suggests otherwise. The neat thing here is that this leaves the viewer in the position of being able to pick the decade for a "historical" stardate as he pleases!
In the end, then, the TOS gimmick of using nonsense dates has made it easy and convenient to maintain the Trek timeline. And the later DS9 and VOY practice of failing to mention the stardate at all in the episode makes things even easier.