One concern about fanxpert2 is that it is tied to the Aisuite bundle, which has had anecdotal reports of causing other problems that were solved when it was uninstalled. With the maximus hero, as a backup plan, would it be possible to run the fans at low speed without aisuite and fanxpert2 installed? Not that this would be an ideal method, but in theory could manual fanmates be hooked up to all the fans, and then the voltage could be lowered manually? That would probably trigger an error message in the bios, but if so, would that only occur at startup and then it would run fine and quietly? Or would it not allow it? I just wanted to know if this was an option before giving up on this board, as it otherwise fit the bill.
Asus higher end has very high restrictions on pure bios even on the CPU, but all get overpassed once FanXpert2 loads. But i guess will depend on the fans you chose, for example there are fans that even at 12V are quiet like Scythe Gentle typhoon 500/800rpms.
Now MSI is not that hot on bios if you going for 3pin fans, there is a 50% restriction on bios for CHA_FAN headers, but if you chose 4pin PWM fans and use CPU_FAN1 and CPU_FAN2 headers, they are capable of dropping to 12.5% at the least, with increments of 12.5%, that's what im doing atm, with a Y PWM fan splitter, i really like this solution and probably will continue to persue this type of setup, as its very nice not to depend on extra software or even the OS you are running.
Asrock also seems like a good choice for pure PWM fans, although i haven't tested personally, it seems it has much more tweakability on the % and breakpoints, more than MSI, that said, i still like a lot my MSI, its been great for almost a year, while i had a ton of issues on my Asus Maximus VI Gene, like audio clipping, stuttering among other things, and the high bios restrictions made me move to MSI, no regrets, but i still recommend asus, its by far the simplest way for someone to setup a quiet pc, specially for using the included fans that most of the time are 3pin.
There is also speedfan as an option if you don't want to use fanXpert2, but just be careful into choosing a motherboard that its sensors are supported.