I'm rigging a Corsair 360 AIO in push-pull (6 fans total) for my 9900K. 3 of the radiator fans are controlled via AIO_CPU fan header on my motherboard, an MSI MEG Z390 ACE. The AIO is also connected to the PSU via SATA cable.  I want to control the remaining 3 fans through my case's built-in PWM fan controller, a Fractal Design Define S2. However, the manufacturer's manual instructs me to plug the PWM fan controller cable into the CPU header on my motherboard. This is not an option because my motherboard doesn't recognize it plugged into the CPU header. I am already using the AIO_CPU fan header for the AIO so maybe it doesn't allow simultaneous CPU fans, but that's speculation and I really dunno. It could also be broken. Anyways, the PWM fan controller for the case is also connected to the PSU via SATA cable same as the AIO.
My question is this: are chassis fan headers on the motherboard safe for a PWM fan controller powering 3 fans? Can chassis fan headers provide as much voltage as CPU and PUMP headers safely?

If your fan controller has a SATA power port, likely the PWM to mobo connector is only sending/receiving data for speed control and is not loading up the header with a full load.  Otherwise it would be pointless to have a SATA connector on the controller.  Does your fan controller have enough open ports to connect all 6 fans from the push/pull set up to it?  then you could just run the fan controller cable to either cpu fan or aio fan header as desired.  The BIOS is probably (guessing) expects that if you have something connected to the AIO header then you wouldn't have anything connected to the cpu fan headers but only they can tell you for sure. 
 
For reference my Asus board has AIO and chassis fan/etc headers and ALL of them are only 1A so I assume stuff like AIO headers have extra BIOS functionality to link to specific functions like labeling it as pump speed instead of fan speed for example or something.  My board does also have two separate headers that are listed as high current 3A headers though and that's very specifically called out in the manual.