Maybe that’s why they put the little quarter note next to the bpm in the transport- It’s always to the quarter note. Also it permits people who want to to have insanely fast metronomes, like quarter = 2400 bpm with a denominator of 32. It sounds like a 40 hz tone. 
edit: and you can get an A tuning note with 206.25 bpm with a denominator of 64
But, as of 9.5 they have added advancements to the metronome, now you can set it up sensibly, using the new click patterns.
Also we now, finally, have actual correct compound time signatures, and can adjust the grid to follow.
You linked to the 9.0 docs, which talks about the countbase. My contempt for that “feature” cannot be expressed with mere earthly words. 
check out the new feature: Metronome Setup