PCIe is also packet-based BTW [1]. The benefit from the custom protocol is being able to run PCIe and DisplayPort (and I guess networking which no one cares about) over the same cable at the same time with dynamic bandwidth allocation. USB-C has alternate modes but they're not as powerful. In theory PCIe alternate mode over USB-C should be possible and it would be much simpler than Thunderbolt but nobody has tried to build it.
I imagine the spec doesn't really exist because Intel has been too lazy to properly write it (I wouldn't be surprised if Thunderbolt is basically defined as whatever the original Ridge controller implemented) and it's probably also gross. Adoption seems to be limited by cost, not by secrecy (thinking back to Firewire, it was open but there were very few controller chips for it).
Probably also timing etc. - I would think making it packet based is probably easier to make work over longer cables than raw PCI-e.
The bit I really don’t get is why they keep all the specs secret. What do they think they have to gain? All that it has meant is less adoption...