I am more than happy with my TKO 600. I had the same concerns about cutting the tunnel... but I do everything backwards and decided to upgrade the tranny after the build was done and the interior was in.

That made my decision a little easier.
I know everyone loves their T56 and it probably shifts a little better but for me, so far, I dont see the need. It is fine on the highway. I run 3.73's with a 19" wheel (dont recall how tall) and the RPM's are in the 2100-2600 on the highway which I am fine with. Not sure I'd get it into 6th often enough.
The mileage and smileage is way better than with my old Muncie. So much more enjoyable to drive.
You cant go wrong either way.