An internal PCIe slot can be had in up to 16x 5.0, whereas Thunderbolt 5 maxes out at 4x of 4.0. Plus you have another Thunderbolt controller in between the CPU and the hardware, and it takes more energy to push that many bits 1m over a cable vs a few dozen cm over traces.

Also Thunderbolt is trivially disconnected, which in many critical workflows is not a positive, but an opportunity for ill-timed interruptions. Plus I don't have to buy a fucking dongle/dock for a real goddamn slot, make room for external power supplies, etc.