From browsing the manual, it also looks like you can set a Max CPU Temp, Fan Max duty cycle and Fan min duty cycle. Am I missing something here?
This is my experience only with GENE IV and GENE VI, with 2x Noiseblocker 120mm PWM fans PL-PS. With bios no matter what setup as preset (slent, standard turbo) had no effect on the fans (on both GENE IV and VI), the minimum rpms on the bios seems nice I blelieve the last is 200rpm to 600rpm, but dont do anything to my fans either, the PL-PS can drop down to 650 or so, manual with temp threshold didnt do anything to it, still my rpms on idle are 900-950rpm and when the temp goes up it the rpm increase to 1100rpm or so. Overall its not a bad setup, this is how i ran it for 2 years on my GENE IV, as i couldnt control the frontal fan with fanxpert1, the setup was very quiet, but not innaudible, this is what the new GENE VI with fanXpert2 brought, now my frontal fan 180mm idles at 430rpm (before was 600rpm undervolted with fanmate2), my Noiseblocker PL-PS fans now idle at 630rpm isntead of the 950 restriction that was the lowest i could achieve on bios in both boards.
Now i just did a build with MSI Z77-G43, and the bios was better in fan control, while asus has similar values their behavior was not reflected thrully on the fans, while on the MSI i did see each preset handling the PWM fans lower and lower, i couldnt use the lowest out of one fan started to click, so i had to stay one before the last.
One thing worh mentioning is that the PL-PL on the FANXPERT2 graph stared at 630rpm at 0%, not like the chart above where 0% there is no rpms, so could be that the fans that i used cant be used on bios to got that low cause of the restriction that bios has, i bielive its like 20-30% as the minimum, so take my comments with a grain of salt could be that the fans are design differently that i cant drop them as low on bios and i need FanXpert2. I never really tried this fans on the MSI motherboard, nor i tried scythe fans on GENE IV or VI, so could be the fans that are not allowing the drop on pure bios.
But out of my limited experience, im going to recommend more MSI on pure bios, it did work fine with Thermalright TY141 (macho fan) and Scythe Slipstream 120pwm, the TY141 was able to drop to 700rpm, same that i was able to achive on my intel mobo on pure bios, the msi was able to drop it lower i believe like 630rpm but in ther the fan clicked, so i had to pull the setting one up in the bios. But if i had only scythe slipstreams PWM i could have easily used the last preset, the slipstream should have gone below 600rpm.
If you go with ASUS share what you experience and with what fans.