There is no reason why when Adam and Eve were driven out of the Garden they stayed nearby, so there is no geographical reason to dispute that particular point of Mormon theology.
There is no reason - none whatsoever - to assume Mitochondrial Eve and the Biblical Eve should be identical. She is merely the last joint ancestor (in the female line) of all humans living today, not the first human.
As a secularist (yet devout) Mormon (and of course the board's resident Mormon), this is basically my view. You can head on over to my "Let's discuss Mormonism" if you want to talk about other Mormon-centric topics.