I mostly utilize the fan control settings in the BIOS rather than rely on any separate third party software. I have found it to be just as reliable and I do not have to deal with having disparate applications across Linux and Windows (e.g. fancontrol on Linux with more manual configuration, see our lm_sensors package and this guide, which while targets Ubuntu is still fairly applicable -- versus AMD Ryzen Master Utility on Windows).
Most BIOS / UEFI even have a lower RPM mode, sometimes named "silent" or "quiet". They are typically just a slower ramp then an aggressive curve when it starts getting into high temperatures. This is something you can fiddle around with yourself pretty easily. Personally I have the fans at a low RPM, from 800-1000 for 35C-55C, then a gradually more aggressive curve after that. But that works for my system, your mileage may vary. At least from the images I have seen of the System76 Thelio-R2 they have a very custom solution for routing air, so you might not have as much wiggle room.
Can't stand fan or vibration noise myself, vibration is almost completely sorted (save for the HDD cages) thanks to the Noctua NA-SAV2 anti-vibration mounts. Realistically only way I could get it quieter is buying a beQuiet! case (I'd like to get a Dark Base 900, as opposed to the rev.2 since I don't want an acrylic / glass side panel) or going fully passive. (inb4 someone asks about water cooling, I do not want to have to worry about leaks, pump failures, or deal with the added maintainence of draining+refilling the loop, so not really something I am interested in, air-cooling has been fine for me)
