I participated a bit in the discussion while r6rs was being created, but it quickly became apparent to me that the goals that the editors were striving for weren't things that I personally cared about.
So, anyway, due to the "compromise", can we get mutable pairs if we run MzScheme in r6rs compatibility mode?
(import (rnrs) (rnrs mutable-pairs (6)))
(define x (cons 'a 'b))
(set-car! x 'c)
$ ./mzscheme a.scm
(c . b)
So yes, though it turns out that in r6rs compatibility mode cons is really just mcons, so we don't actually gain anything.