What's happening is that the game is noticing that, while Visual Jason is in the same area, Virtual Jason is in a different room entirely, and the game is actually loading the other room while you watch, I believe correcting the discrepancy on the fly. It's really odd to work with and usually destroys whatever manipulation you were going for.
I seriously believe skipping Area 5 in U-Rom is not possible. The dumb door is way up in the air!! Messing with that weird auto-correct mechanic is still worth looking into. If it's not helpful here, it might yet be elsewhere.
Area 3 boss room door glitch: If I remember right, you don't have to pause-unpause; the fade-out-fade-in fixes that for you. Just move a tile over and enter the room and you're good. Still might be slower though, and you might have already accounted for this, so pbbt.
Skipping a large part of Area 4 on the way down to the boss might be possible, I dunno it's a wild idea I just had. You can walk over the water when taking damage (At most two tiles of movement, I think). It might be possible to enter one of the non-boss dungeons, walk over a short section of the water using damage, and reach the boss early. I remember discussion on discovering that it's not possible to go in through the wrong entrance in Area 7, but Area 4's islands are laid out differently, and often closer together.
http://www.auriplane.net/blastermaster/