I ran into the same problem as well - I tried an older version of the script (5.3) from Github and the merge problem doesn't happen with that.

Regarding the other issue mentioned by Naos - any help with that? I get similar results (different behaviour compared to the tutorials: a separate slot for each skin instead of one slot with skin placeholder attachment) and I don't really understand why that is. EDIT: I realized it needs the [slot] tags and then it works as expected, so user error this time