Nah, the PSU controls the voltages. All the motherboard does is turn on the PSU by shorting the green PS-ON wire in the mobo cable to ground. The thunderbolt card actually came with a switch to do that, normally I use a paperclip :D.
http://bitsavers.informatik.uni-stuttgart.de/pdf/intel/ATX/ATX_Specification_2.01_199702.PDF
PS-ON is an active low signal that turns on all of the main power rails including 3.3V, 5V, -5V, 12V, and -12V
power rails. When this signal is held high by the PC board or left open circuited, outputs of the power rails should
not deliver current and should be held at a zero potential with respect to ground. Power should be delivered to the
rails only if the PS-ON signal is held at ground potential. This signal should be held at +5VDC by a pull-up resistor
internal to the power supply.
Here is an example of a switch: https://a.aliexpress.com/_msxxnjv Mine doesn't have the third wire, I think its just for powering the switch LED though.