I agree basically with everything you're saying, but that's not arguing for raw gate netlists. If anything it's arguing for even higher levels of abstraction where clock domains are implicit semantic contexts.
Many new school HDLs are working in this space and they couldn't be farther from the "representative of what digital circuits are constructed from" idea. Often they're high-level programmatic generators, very far from describing things in terms of actual PDK primitives.
In a way is further away, but in another way it's actually closer to how real hardware works: Clock (and reset) trees are real physical things which exist on all digital chips.