If the inputs in the official version were changed to work with arcade machines devs would no longer be able to test or fix the games. That's what derivative builds are for.
it would be satisfactory if there were support for multiple input devices, controlled by compile-time flags. the "official" build could be whatever the mame devs want, and the rest of us could make alternate choices, but there would be only one body of source code.
the problem with the current situation is that any change that the mame devs refuse to accept, but is needed by somebody, requires on-going parallel development and re-merging. for example, mame analog+ adds much value, but it appears that the developer who did all this work does not have the time to continually re-merge it with the official build. if he doesn't keep doing this, it will fall by the wayside as time goes by.
on the other hand, if his changes were in the official build, users who need his work would get the benefit of all future mame work, with little to no on-going work.
the same can be said for every other derivative build.
a "second best" approach would be to roll as many derivative builds as we can into one, so the on-going maintenance doesn't need to be duplicated by many different people.