Hi. Wow. Darkbreeze asked me to jump in here, and I've read the whole post, twice, and it seems to be going around in circles.
The TT controller as far as I can see is rgb only as far as fan speed control goes. There's no fan speed input or output anywhere there.
The 2pin on top goes to the proprietary switch in the case, and has 2 modes. Case mode and software mode.
For case mode, you hook the Sata connector directly to a spare connector from the psu. It's strictly a 12v power source that'll handle the amperage a fan/rgb header won't. Fans plug in where the fans go. You change the RGB by pushing to button to get the desired affect.
For software mode, you'd also connect the wire at the bottom, the 12v,g,r,b wire, that has 2 connectors. One of those will fit the Gigabyte x470 12v rgb header. Push and hold the case button for 3-4 seconds. That disables the built in affects and enables the Fusion sync to work. Now your rgb will be changed according to the software.
But the fans are still at 12v constant. Bios isn't going to have any affect because the fans are not connected in any way to a motherboard fan header. They run at max speed always.
There isn't a way around this without major surgery on the fan wiring. Sorry.
Your only option if you want actual rgb control And fan speed control is forget the whole Thermaltake controller and case switch, and use a standalone or Fusion compatible system with 4pin PWM rgb fans. The fans would be used via powered splitter to a fan header, and the RGB will be used via splitter to the Fusion +GRB header.
But that's the gimmick. Rgb/argb fans are a joke. The motor housing in the fan is only so big. For a regular fan, it's all motor. For an rgb/argb fan, the motor is cut down in size to make room for the rgb/argb wiring and pcb. So considerably less performance ability.
Just far more flexibility (almost all those fans have 2 connectors, one for rgb, one for fan speeds) than the proprietary system TT has in that case.