I think there's merits to both embracing a backroute and for patching them, depending on what the backroute is and what the intended solution was.
If you haven't already, I'm not aware of any rules banning asking for help debackrouting the level (i.e. post your intended solution replay and have someone else take a look and see what they can do to fix the backroutes) - if there is a rule against it, there's definitely precedent for letting it slide, as I've done it before publicly. Unfortunately, R1 blocks a lot of tools you can use to patch such backroutes, but do keep in mind you can always release a new version after the contest that uses those features.
On another topic, I don't see anything wrong with allowing the backgrounds. They weren't present in the original game, sure. But they don't affect gameplay, and there's backgrounds that are designed to fit in with the original sets included by default. Personally, I think it's a bit pedantic to disallow them.