Thanks for the extensive info and tips!
The
"problem" is not that the koth mutator uses fences/walls, but that the koth area counts as occupied as long as any unit of the currently occupying team is still in there.
Since it's comparably hard to remove fences/walls (except if you have a good control of the area and can suck them up with a builder), this potentially throws balance off, i.e. gives an advantage to the current occupier.
Luckily, the solution is not that complicated and just needs an additional
if to ignore these unit types. In the back of my head, I anyway had for a while the idea, to look if I visually improve these maps a bit and re-release them.