Even if Thunderbolt had enough bandwidth, for Apple to go back to that kind of design is just asking for ridicule. For Thunderbolt 4 at 32 GB/s vs x16 PCIe 5 at 63 GB/s also is going to make a pretty big difference.
You have conflated your units.
Thunderbolt 4 is about 32Gb/s ( not 'Bytes', but 'bits'. So that is 4GB/s ). x16 PCI-e v5 is 512Gb/s ( or about 63-64 GB/s ). There is an order of magnitude difference between those two bandwidths. That is more of a "huge" difference than a 'big' one. Handwaving that "Thunderbolt solves the problem" is exactly one the explicitly mentioned (by Apple) 'traps' that they fell into with the MP 2013 (6,1). There is an 'economy of volume' problem with overly relying on Thunderbolt. Folks who have two or three Audio cards , a video capture card or any sort of > 2 collection of stuff piling up enclosures get more awkward to physically provision in limited spaces.
Highly unlikely that Apple is going to touch PCI-e v5 though. But even falling back to v4's 32GB ... still basically an order of magnitude difference.
I think that Apple is going to take a hybrid approach. Unified memory for the first 64-128 GPU cores and then x16 PCIe 5 for any add ons. PCIe isn't going to give 200-400 GB/s but more GPU cores at 63 GB/s is still better than nothing.
If this is a "M1 <insert adjectives here > " SoC the likeihood of PCI-e v5 making an appearance is more wishful thinking than likely outcome. Apple has done some relatively extremely limited PCI-e v4 with the M1 SoCs so far. To jump to v5 with the same gen number attached would be 'odd'.
The other problem is that these discrete GPUs would require new drivers and more GPU customizations because the unified memory assumptions buried in the Apple GPU optimized code would be gone. Apple just herded folks into rewriting their GPU optimizations into the Unified memory format. How happy are developers going to be be to re-optimize for yet another one? Probably not very pleased.
Better chance that Apple is betting the whole farm on unified Memory GPU cores. 128GPU cores will cover a large amount of the GPU performance space. M2 , M3 , M4 generation GPU cores will get improvements so that space is at least just as large , if not more. Multiple GPUs used to attack AI/ML workloads will be pointed at bigger NPUs. Video/Imagine processing of standard camera codecs .. at bigger image compute fixed function logic. high end , interactive 3D ... doesn't really scale that well with mulitple GPUs.
Squeezing better GPUs into VR/AR headsets is also probably going to be higher on the priority list than chasing market where Nvidia is far more deeply entrenched with a wide , defensible moat. Their focus is likely going to be on more GPU performance in smaller volumes not bigger ones.
Apple is much more clever than I am and I trust that they will solve this in a way that lets their customers with crazy GPU requirements get the most out of the Pro. Just for reference, the current Mac Pro has about 140 GB/s memory bandwidth and still uses x16 PCIe 3 @ 32 GB/s for GPUs.
Apple will probably have slots for other stuff than GPUs. GPU add-in-cards are a myopic overly narrow justification for provisioning some slots. Without the drivers it isn't a complete solution and there is zero movement on discrete GPU drivers in macOS on M-series.