A similar sort of thing occurs also on NeoLemmix (and DOS Lemmings), although there isn't any terrain generated by the builder. I can confirm on one of the Lemmings Plus III levels that if you place the builder in a certain place he does avoid the exit, but lemmings walking from either side can go in.
Personally I wouldn't "Remove the lo-res pixel and add a pixel at the tip of the bridge, keeping the shape" because I like the simplistic detail of each brick. To be on the safe side I would keep the design as it is, just in case if there happens to be a level that require backstepping in order to be solved. If you want to make the mechanics more akin to Lemmings then the second option of removing the lo-res pixel would be fine.