I accidentally played the game on "extreme difficulty" since I didn't notice that it's possible to cross conveyors and flip branches. So I had to invent special solutions for situations that wouldn't arise during "normal" gameplay.
I'm so incredibly glad I found this post, because I've been doing the same thing and finding myself spending more time trying to logistically fit everything without crossing paths. This should save some time (although I do kind of enjoy the logistics challenge that is trying to fit everything in without bridges). =]