They exist to partition capability so that enterprises can’t connect all of their peripherals and some ECC memory to get the same functionality for 1/10 the price. It’s not a physical limitation.
Obviously market tiering is part of it and you can play tricks with north and south bridge and pcie switches (which adds cost), but a ryzen board that advertises a pcie 5.0 x16 gpu slot and 5.0 x4 m2 slot only has 4 lanes left to work with from the cpu (i.e the cpus only have 24 usable lanes). Which while you can play with generations to get more lanes it's effectively still 16gb/s. That needs to cover network, extra m2 slots, usbs, as well as the extra PCIe slots.
I don't mind having to work within those physical limits but I do want to be able to search for boards that support N components. i.e 1x 4.0x8, 2x 3.0x8, 4x 5.0x4 . But the best you can search for is physical sizes of pcie slots and then dive into a spec sheet for each one, only to find that the 6 x16 slots only have 1.0x1 of bandwidth each.
I think the biggest aspect is that there’s so little demand for the configuration that you’re looking for.
Most people only need the PCI lanes for graphics cards and storage. There aren’t many other internally installed devices out there that actually need that kind of bandwidth, and a lot of those use cases are already covered by alternatives like Ethernet or USB, or they’re already on your board (m.2 slots, fast Ethernet ports).
The 6x16 slots with 1.0x1 bandwidth are there so that people can plug in stuff like sound cards and other random stuff that generally has pretty light bandwidth needs.
If I just search for “PCIe card” on Newegg most of the resulting products max out at x4, and most of the ones that do are already on the board (m.2 cards, additional USB/Thunderbolt).
The one use case that seemed useful and unusual in my search results was a quad port HD video capture card which seemed to require x4 bandwidth.
If you had a scenario like you describe where there isn’t a single x16 slot, you’ve instantly annoyed 95% of the market that needs that full bandwidth for a GPU, whether it be for gaming or for professional applications.
Some solutions that avoid expensive workstation boards and CPUs include getting a higher end chipset to get gaming boards that come with 2x x16 slots, or you can use accessories and adapters that just plug into m.2 slots.
I don't mind having to work within those physical limits but I do want to be able to search for boards that support N components. i.e 1x 4.0x8, 2x 3.0x8, 4x 5.0x4 . But the best you can search for is physical sizes of pcie slots and then dive into a spec sheet for each one, only to find that the 6 x16 slots only have 1.0x1 of bandwidth each.