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Nope. I actually did that unintentionally on a PC I built. I only used one power wire when the GPU needed 2 so it couldn't use all the power it needed when running 100%. My understanding was PCI doesn't support disconnecting devices so the system expects all components it starts up with to be available all the time. Lose one and the system goes down.
PCIe absolutely does support disconnecting devices. It is a hot swap bus, that's how ExpressCard works. But it doesn't mean that the board/uefi implements it correctly.
in other words: OP either needs to get a thunderbolt dock or straight up have 2 computers. The latter should not even consume that much more power if the PC gets shut down in the evening and woken up using wakeonlan in the morning.