The only manual focus camera with this feature I've ever personally encountered is the Canon AL-1. There may be others, but that's the only one I know of.
I'm PRETTY sure my Pentax 645N will give focus confirmation with manual focus, but I've not actually tested that as I only have AF lenses for it. My 67-645 mount adapter did arrive today, so I'll see if I get it once i have a chance to test that.
On the whole, AF medium format SLRs are a pretty small subset of medium format cameras made. Offhand, there's what, the Pentax 645N, Rolleiflex 6000 series, Hasselblad H1, and maybe one of the Mamiya 645s? I feel like I'm missing an obvious one in there, and there are probably a few others I'm missing, but they're definitely not the norm, and all of them are pretty late to the game compared to AF 35mm(and about a decade behind on AF tech-the 645N is the only AF I've used, but that 1997-released camera has AF that reminds me a lot of the AF in the Nikon F4).
At the end of the day, focus comfirmation like on the Canon AL-1 uses I think a 5 pixel CCD(or maybe 3 pixel?) that sits under the reflex mirror and looks at contrast on the adjacent pixels. An autofocus system starts with that and sticks a motor on the focus mechanism to get it there on its own. Of course it's a lot more complex now(my D5 has I think 151 AF points?), but the focus confirmation system is really already 2/3 of the way there to an AF system. Pentax basically did the same think on the 645N as they did on the K mount(and Nikon did at first on the F mount) and stuck a screwdriver blade on a motor to crank the lens focus in and out. If such a beast exists I can't imagine the camera not just going ahead and supporting AF in some form or fashion. The only place I could MAYBE see it happening-and someone can correct me if this exists-would be on one of the lower end Rolleiflex 6000 models, but then from what I've seen that's not exactly a cheap system to get into with any body...