For example discovering that two phenomenon we thought were separate are actually sub-cases of some more basic phenomenon.

I like to do this a lot in mathematics, but fortunately mathematical language is both rich and rigorous enough that I can avoid false alarms in that context (category theory in particular is full of examples of phenomena that look separate but can rigorously be shown to be subcases of a more basic phenomenon).

I think of mathematics as being a conspiracy theorist's fantasy land: it works nearly the way a conspiracy theorist thinks reality works.

So I guess what I'm basically asking is why aren't we spending a lot more time improving the checklist of rationality habits, especially via empiricism.

Well, that's something like what CFAR is trying to do.