There are companies putting nonstandard PCIe ports on the outsides of laptops, and compared to that an internal custom port is much less egregious. 40Gbps is just not enough to run a GPU without significant performance loss. Especially when 40Gbps is actually 32Gbps of PCIe and on older controllers there's an arbitrary limit of 22Gbps.

I really hope thunderbolt 5 in asymmetrical mode can devote the entire 120Gbps of outgoing data to PCIe, and doesn't have some stupid limit like 64Gbps.

And when a new standard amounts to "arrange the pins like this", it's not a very big deal.