5xxx <-> 6xxx differences are non-existant- any differences you saw was inherent to the board revision used.

when one puts a x400 board in a aio chassis, the harness assembly lets the board identify as a 5400, in the instatower chassis, it's a 6400

this is based on the same gestalt selector concept present in other macs such as:

580<->630

475<->605

7x00<->8500

etc, etc

same goes for any other x2xx-x5xx board