Hi!
No idea why combined mode is the default, it's only useful for OSes from the '90s. It's not about the type of drives (SATA vs PATA) connected but how the SATA controller identifies itself to the OS.
I agree that the combined mode isn't the best default, but I can't say that it's totally useless. In combined mode you have the first 4(?) SATA ports connected to an AHCI controller and the last 2(?) to a legacy IDE/ATA controller. I had some SATA->PATA bridge to connect a PATA device to a mainboard and the adapter I had only worked on SATA ports that were connected to a legacy IDE/ATA controller, but not on SATA ports connected to an AHCI controller. I didn't further debug that issue though, so I can't say why it didn't work on an AHCI controller.
Speaking of the KGPE-D16: I still have this patch [0] in my review queue that is needed for coreboot to work on the board when the BMC firmware flash is installed, but it seems that neither Timothy nor owners of that board really care about that patch any more (I poked a few people about that patch a few times), which I find quite sad. Would be good if someone would address the last 3 comments and actually tests the patch on the real hardware, so it can be merged to fix that show-stopper.
Regards
Felix