I'm finding that the mod loads in pieces... somehow. If installed by instructions given, rebalances to the characters' abilities apply (except for fish's extra gold), but the new starting weapons don't and the free item chest does not appear. If I *incorrectly* install it to the NTT mods folder, the free chest appears and these abilities load as well, but the new starter weapons attempt to load and become errors instead with the exception of the rusty revolver.
Seeing that the mod seems to load some parts properly in either place, I loaded the mod *twice*, once paired with DW and once from the NTT mods folder. This seems to give me a complete package, including the extra gold from fish. Nothing about the install instructions suggests this is how it is meant to behave, and I'd imagine I'm probably doing something wrong somewhere. I suppose if anyone is having this same problem, this is the solution for now.
I also haven't tested this behavior with the mutations expansion, so for now I'll play it safe and expect that any potential issues could be fixed by loading it twice.