Currently there are no differences between the normal branch and the experimental branch, except that logs are written on the experimental (Which can actually lead to it being slower if there's some kind of infinitely repeating error the computer is having to write to the log file every frame), so main should actually generally run better.
Pathfinding issue's we're not cataloguing at the moment as we're reworking the whole system, which should hopefully fix a lot of the problems people have been having. For issues like the one you're describing you'll unfortunately have to rely on in game tools to alleviate the problem. Telekinesis is your best bet, as you can sometimes use it to reset the pathfinding on a single nugget. However, it doesn't work all the time, is tedious to use, and uses CP that leads to nugget Fear (Which if you're doing a Fear run, is a bonus I suppose) meaning we recognize it's not ideal.
Hopefully soon we'll have some brand spanking new revamps to fix it all, but until then we'll all have to get by with what we've got.