It's not really a problem as far as they are concerned. Parks with such immersive themes are designed around focal points. The average guest doesn't see (or care about) being able to see the Antarctica or Forbidden Journey show buildings unthemed. They may notice a building but don't necessarily know what it is, and more importantly don't pay it much attention as their attention is drawn elsewhere. In Jurassic park most guests who are actually looking around and taking it all in are enjoying the foliage and discover center ahead (because they really are in Jurassic park) not paying attention to what is on the other side of the trees.
They don't care that transformers, mummy, spider-man, cat in the hat, journey to atlantis, small world, peter pan, haunted mansion (from the right viewpoint), mission space, soarin, and so many more rides are clearly in the large unthemed buildings behind the themed front. Their attention is drawn to the points that the designers intended.