I have a pretty custom GPU cooling setup on a few machines (I run ML workloads locally and I want stuff to be quiet).

Couple of gotchas that I ran across. I found that on Linux, desktop PC fan control support is pretty abysmal. The sensor library that everyone relies on, lm_sensors, is semi-abandoned and didn't recognize sensors on my relatively popular, 7 year old ATX motherboard and GPU. It also requires having Perl installed.

About GPU cooling in particular - modern NVidia cards in particular seem to have a built-in minimum of 30% fan speed when controlling them manually. The connectors are also a different, smaller connector (perhaps a JST PH?).