What is this issue with fans always running at 12v?
Well most of the time, depending on the fans themselves, they are louder at 12V, not saying the Glidestream are but its nice to be able to undervolt (in your case with fanXpert2) them or control them via PWM, at least under light load or idle, so you end up with quieter setup. Todays intel cpus they generate very little heat on idle or very light conditions, they do run hot under load, so having control based on the temperature of the CPU is ideal to have the most quiet setup under the circumstances its facing.
So, you are saying if it is on auto fan xpert 2 would not be able to properly control all of that?
I think you are confusing what the word means with a the "name" that Asus assign to a bios function. Auto doesnt mean its automatic, just means the fan header is setup for PWM fan control, aka 4pin. Advanced, the other "name" that Asus gave to the setting on the Q-Fan on the bios, is simply to not control the fans with PWM control, but to change the settings to voltage control, in plan terms it will undervolt them. Overall both work fine, i personally prefer PWM as i usually search for fans that have a huger range of PWM rpms, but this is not to say the 3pins are bad or inferior, its just a different way to control the fans, both work really well, given you chose the correct fans and settings on the bios.