Probably some sort of weight limitation, I'll bet. And I'm guessing that notice not being on previous Gundersons was an oversight; the Pecos River Brass bulkhead cars carried that warning years ago.
More likely that a 20 foot container should NOT be loaded in the space for a 45 foot container.
Sorry, but on these bulkhead cars, the bottom well will only accommodate a 40' container!
The bulkheads may make it difficult to unload 20's, i.e. only certain types of loaders may be able to grab them and not all facilities are so equipped. Since there are so many non-bulkhead options available now, just don't load them in that type of car.
This would beg the question, why would MTH sell their sets with two 20's on the bottom and a 40' on top? Maybe they didn't get the memo.