Most of things that changed would be really small or minor details. The design of the articulated joints over the trucks changed around maybe 2000, for example. But Kato's representation of those joints is too imprecise to matter, unless you want to 3d print replacement parts (something I've thought about doing for functionality more than aesthetics). There may have also been minor changes to handrails and things like boxes to store IBC connectors, but again, those things aren't really on the Kato model.
The only more noticeable thing that changed with some 5-unit intermodal stack cars of the earlier era was that they started out with a single brake wheel at the B end, but eventually got a second one added at the A end. That said, I wouldn't go removing the brake wheel at the A end unless you find a clear prototype picture to corroborate. I can't remember off-hand if this applies to any early Maxi-Is.
In my opinion, the paint scheme (and patched reporting mark, if any) indeed defines the era for these cars above all else.
