Just to throw my anecdote in: I used to work at the mypy shop - our client code base was on the order of millions of lines of very thorny Python code. This was several years ago, but to the best of my recollection, even at that scale, mypy was nowhere near that slow.
Like I said, this was many years ago - mypy might've gotten slower, but computers have also gotten faster, so who knows. My hunch is still that you have an issue with misconfiguration, or perhaps you're hitting a bug.
My current company is a Python shop, 1M+ LOC. My CI run earlier today completed mypy typechecking in 9 minutes 5 seconds. Take from that what you will.
Ditto, same order of magnitude experience; at least for --no-incremental runs.
Part of the problem for me is how easily caches get invalidated. A type error somewhere will invalidate the cache of the file and anything in its dependency tree, which blows a huge hole runtime.
Checking 1 file in a big repo can take 10 seconds, or more than a minute as a result.
Like I said, this was many years ago - mypy might've gotten slower, but computers have also gotten faster, so who knows. My hunch is still that you have an issue with misconfiguration, or perhaps you're hitting a bug.