I'll at least give them a bit of credit for lowering the Soarin building as much as they could. As you go through the queue, you walk quite a bit downhill. That monstrosity could be much more intrusive. I still don't like it, but they tried.
Universal hangs their hat on the "we're a working studio" mantra when they let show buildings hang out all over the place. DHS is the same way. They'll put up some nice facades, but then you see warehouses (wait, I mean soundstages) all over the place. I don't know if it's them being cheap, or honestly trying to live up to the "backstage" nature of it all.
I see Potter as being similar to ToT, in that they're not "backstage" themed attractions. WDW did a fantastic job of theming every square inch of ToT (including the modifications when they built Fantasmic), and rightfully so. Uni should have spent a few more dollars on Potter. It's such an immersive land (so I've heard), that it's a shame to have a warehouse sticking out.
Regarding Main Street and HM....I see those as mere oversights or accidents. When they built MK, they spared no expense and tried with all their might to hide this stuff. You only see HM because of the lack of foliage these days. A few more trees and it would disappear. But it's still painted natural green and somewhat disappears. They probably could have extended the Main Street facades a bit further by Tomorrowland, but perhaps they just missed that one line-of-sight when laying everything out. I give those early Imagineers way more credit than today's. Today, they'd see it and go "Meh, saved $50,000 in facade construction." Back then, they probably walked the park after opening and said, "OH $#!+, put that on the list to fix!"