the super io chip is pretty universal. it's position in the scheme of things is just to provide connectivity for the parallel, serial, floppy, keyboard, and mouse connections. it's not driver specific as the data is effectively handled by the southbridge.
as long as the southbridge, northbridge, and audio chipsets are similar/same it's shouldn't get too complicated to swap.
mahkeymike has been doing some chopping regarding the software and loading new drivers to use other boards. He's far more versed in linux than I am, I haven't a clue when it comes to linux...I'm a DOS dude.