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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.
Also some GPUs support running without the external power connectors/not all of them. My old GTX 1080 ran for about 3 months off of just the PCIe slots power because I forgot to plug them in. Newer GPUs are FAR more power hungry though and not all newer cards support that. Plus I've never tried yoinking the power cables while it's on. That can't be good.
Oh nice! I knew hot swapping was supported on many other devices but not PCIe itself. Feels wrong to rip a card out while the system is powered up.