Interesting, and complicated. Safe bet would be use all the same brand fans, so the PWM signal isn't different.
Yes, but you can work between brands as long as you know the range of operation on PWM singal. And on "PWM signal isn't different" is not that its different, the PWM singal send by the CPU_FAN header is the same for all, its the fans that are design different, meaning some will be 600rpm under 10% pwm signal and some will be 200rpm, etc, this is what would happen on chosing different fans if you dont plan accordingly, this would be avoided if you chose the same fans for all slots, but this is not completely needed, its just easier.
Since all the fans currently are 3 pin, my cpu fans, my 180mm case fans, I think I might be better off getting a fan controller.
Fan controllers has been the easiest way to control fans for years, so its a safe bet, you just use 3pin fans and leave them to steady rpm to whatever the fan can go to or the fan controller can lower the voltage, and change it manually according to how much noise/cooling you want, but to me automatically fan speeds according to the CPU temperature is what im in to, i used a lot of fan controllers in the past, and i never move them, so i always leave them at a steady voltage/rpms, so i prefer i dont have to interact with it and let the motherboard change the rpms when the temperature is rising, but all this will come with careful planning and chosing the right fans and motherboard.
The controller you linked looks cool though. Maybe there is an adapter that would do the same thing, not using the front of the case though
The FT02 has a ton of 5.25 slots, so i would use one of those, that said, there are 3.5 versions (i cant find one atm online but there was a diskette size) there is also the PCI version that i think controls 2 fans if im not mistaken, Sunbeamtech PL-RS-PCI Rheosmart PCI Fan Controller
considering the whole thing has nothing to do with the knobs when you switch it to convert to PWM mode? If I understand it correctly.
In theory yes, but i dont know for sure as i dont own one, but i would find convinient the knobs for let say you are using a tons of fan, different or the same, for example the FT02 has 3x AP181, each would go to its own connection on the sunbeam, but let say you doing heavy encoding and only the CPU is getting taxed, you can leave the one that cools the hdds and gpus in PWM/Voltage mode and just unleash the 3rd AP181 and pump the speed of it to cooler more the CPU, etc. And even then let say you have other CPU fans, and you dont like the low rpms the controller is given by default, you can also take them out of the control and still use the knobs. Again all is about preferences and what you want to achieve, but careful planning is important so you end up with multiple solutions to what you will face.