I can see it affecting how Bethesda designs the next TES game. For example, if Valenwood is the next location, Bethesda will have to design Valenwood based off what Zenimax does with Valenwood. If Zenimax puts in some major location in Valenwood, it'll likely appear in the single-player version since it'll be a part of the lore.
They really have all the artistic license they want. 1000 years is a long time. Architectural styles and such things tend to change and new regimes would like supplant the old. Disasters can happen that alter the provinces' assets. Wars can destroy cities and things like the Oblivion Crisis and the Red Year can have untold effects.
In short, I wouldn't worry about the art direction being affected too much.
If anything the MMO seems inspired from the games. Ordinator armor and nearly identical Orcish Armor for instance are in the scans and very much resemble previous armors. Which is actually kind of odd considering the wild changes in the various armor types from game to game and it being set 750-1,000 years in the past depending on which game we use as a base for comparison.