This MOD adjusts vanilla collision boxes they have bit large size dramatically.

But, it makes entities like pipes they are clearly connected be passable too (Unlike walls.).
It might be differentiation for convenience.
However, originally they are reliable connected entities.
Basic specification shouldn't to lost for convenience (without rational reason).

Although, existing users might likes to through between pipes.
So i hope an optional settings for pipes( and other ?).

I think of it as having ladders & walkways above the pipes so you can climb over them.
In any event, if you want to disable the pipe edits, you can extract the mod and open up config.lua and remove the line containing the ["pipe"] entry.

Does it allow enemies to also pass through pipes?

I'm actually not sure. If their collision box is the same size as the player then I'd guess yes.