Yeah, the MiSTer project is really just a loose collection of people with a loose common goal. So the true accuracy of cores does vary a lot. Most users don't really care, as long as they provide a pretty accurate experience. I think most MiSTer owners (myself included) prefer it over emulation due to having no lag. I also really like that the MiSTer does not buffer any writes, so there is no shut down. Just turn it off when you are done, allowing my setup to be very console-like.
That tracks with what I thought. Great to know about the NeoGeo!