I've built about 9 computers in the past 4 years and have run various flavors of Linux on all of them (mostly LTS builds of Ubuntu), and I've never had compatibility problems with the motherboard. Nowadays nobody can really afford not to support Linux, so I think the important thing is to wait a little while for the chipset drivers to get integrated into the newest builds of the Linux kernel, and then go from there. I've had issues with USB 3.0 support for an older CentOS version, but overall everything works for the most part. Linux even works better out of the box than a clean install of Windows 7 sometimes, because Win7 doesn't have drivers for a lot of common NICs, whereas Linux usually did. As you mentioned, in the latest computers I've built, the UEFI did give me more problems than traditional BIOS, but they weren't show-stoppers by any means, just a google search away from a resolution.