To an extent - but a few people still need PCIe slots for specialist I/O, audio/visual and networking cards or to add large quantities of internal storage. That's the only reason for buying a Mac Pro post-Apple Silicon. The PCIe bandwidth/number of lanes/number of slots supplied by the Mac Pro still greatly exceeds what you can get from a Thunderbolt 3 to PCIe enclosure. Thunderbolt 5 might help a bit, there esp. for PCIe 4 capable cards once suitable enclosures appear.
If you submit to Apple's "integrated GPUs rule" theory then 16 lanes is a fairly generous provision for specialist A/V cards, network cards and SSDs - which is all you can plug in to the Mac Pro.
Your typical x86 system will need at least one discrete GPU which will eat 16 lanes. High-end ThreadRipper Pro machines (...and even the old 2019 Mac Pro) will often have multiple GPUs each sitting on 16 lanes which is the main reason that Threadripper, Xeon-W etc. need so many lanes.
I disagree with this in part. For me, having fast u.2 storage and fast networking make the studio a non starter. PCIe5 based u.2 drives are now between 60-120tb of storage. And are super fast. Best bang for buck at fast speeds by far. The 16tb offering in the studio is likely stuck at PCIe 4 speeds, and for that price you can likely get two 30tb U.2 drives that would trounce apple's offerings both in speed and capacity.
Anyway, the controller cards like from highpoint are 16 lane just for the SSDs. Then if you want state of the art fiber networking, which is now up to 800gbe, youre going to need 16 lanes as well. And, this is not crazy, if you want two cards so you can really get crazy bandwidth on the SSDs, you'd like another 16 lanes.
So while I agree with you some of the still good use cases for a Mac Pro with PCIe slots are storage and networking, even if you need zero GPU prowess, the number of lanes in the 2023 are just on the anemic side. Sure, it's better than nothing, and even if you share some bandwidth, on average it will still be much better than what a studio could do via TB5, but it would be nice to increase the number of lanes a bit.