So what? of course they weren't intended to be obvious, but then again neither was leaving Jabba in ANH on the cutting room floor. Lucas had obviously intended to put it in if he'd shot the scene... going with what was in '77, though, the matte lines and boxes, the orange blob under Luke's speeder were all there.
Considering the availability of "deleted scenes" on DVDs these days, it should've been more obvious to you that it is extremely common to shoot more film than you need, so you have a lot to play around with in the editing room. Shooting a scene does not in and of itself does not mean that it should be part of the movie. So that's a bad argument to make there.
I think preserving the matte issue is kinda ridiculous. We're not talking about something that is a result of special effects limitations of the day. You don't see similar issues popping up throughout the film (not that I'm aware of). Somebody screwed up, and the crappy mattes made it into the finished film. As sort of a side thing, I can understand the preserving of the mattes in order to keep that "opening night" feel, but as far as the finished film, no.
If we were talking about fixing that scene where the guy in the storm trooper outfit whacks his head, that would be too much, as it would involve taking drastic measures to fix a real-life scene, something that happened on set and was recorded to film, and kept for the finished movie. The mattes, on the other hand, are the result of somebody in the SFX department being asleep at the wheel.