I'm replacing the rear differential on my '98 Freelander for a new one from Ashcroft. When I removed the old diff the Haynes manual told me to mark the flange on the diff and on the prop shaft, so you can place it back the same way as it was.

Since I am replacing the diff a marker would not have any use. So my question is does it matter how I attach the new diff to the prop shaft?

Well I haven't reference marked a diff/prop flange in 35yrs.
Obviously you have no alternative when fitting new.
Different matter if you split two halves of a balanced propshaft though.