Should they be 28"? Does it depend on era? Should all 85-89' flats have 28" wheels?
No, no, and no.
28" (and other smaller wheels) wheels are used on cars that have lower decks than normal (which is part of an over design to lower the total height). In the case of 85' and 89' cars, you'll mainly see this on tri-level autoracks (that have lower decks, not the MTL cars). Heavy duty flat can have 28"-33" wheels depending (don't think I've seen less than 28" but maybe 26"?).
We've covered this a few time here, IIRC, the only auto rack or trailer flat that would have 28" wheels based on it's prototype would be the Exactrail Vert-A-Pac car.
Jason