I think the Toyota MR2 had a real clutch on its paddle shifters too. A real rally car does not have synchros... which makes it harder to drive on the street. Even the STI and Evo are toned down for street use.
You're correct, the MR2 does have an electrohydraulically controlled manual, so it does have a clutch, no clutch pedal though.
You're right about the rally cars too, they don't have synchros, but they don't have manuals either, at least not H-pattern manuals. They have sequential shifters similar to a motorcycle, most of them have a lever that you pull back to upshift and push forward to downshift, some have a ring on the front and pack of the steering wheel that you hit to up and downshift.
The Subaru Impreza WRC actually does have an H-pattern manual, but it's electronically controlled again, but it has the advantage of being able to shift directly into first or reverse gear in the event of a spin, whereas the other cars have to shift into every gear on the way down.
Hehe, sorry for the long post, huge rally fan here.