I'd expect most of the new motherboards to have AHCI set as the default. The only reason you need to run the controller in IDE Emulation mode is if you're using an old OS like XP which doesn't have built-in support for AHCI (and even then it's a fairly simple matter to load the AHCI driver from a CD during the install process). So for most new systems AHCI is what ought to be used anyway.
I have the GIGABYTE GA-Z68Xp-ud3
I don't think that it was set by default.
I think it asked me something when I first turned on the computer for the first time about AHCI but is said like AHCI/raid and I think that I ignored it.
This was before I even installed the OS just turned on the PC to make sure all was running.