I think these ideas would be more creature comforts rather than actual problems to be solve immediately.
1. allowing conveyor belts and walkways to have their own rules to the encroaching mechanic.
examples: 1a. Being able to place/snap walkways and conveyor belts directly on top of splitters/mergers and on top of machines.
1b. Being able to place walkways/conveyor belts within the encroachment areas of a machine, but not clipping into the machine. Able to fit between two close machines, but higher than ground level.