This was a nice intro to AT (though I feel it could have been a bit shorter)
The whole things seems a bit over engineered with poor separation of concerns.
It feels like it'd be smarter to flatten the design and embed everything in the Records. And then other layers can be built on top of that
Making every record includes the author's public-key (or signature?). Anything you need to point at you'd either just give its hash, or hash + author-public-key. This way you completely eliminate this goofy filesystem hierarchy. Everything else is embed it in the Record.
Lexicons/Collections are just a field in the Record. Reverse looking up the hash to find what it is, also a separate problem.
I'm not sure I understand your proposal. Do you taking my example (a Twitter post) and showing how it would be stored in your system?
Yes. SSB and ANProto do this. We actually can simply link to a hash of a pubkey+signature which opens to a timestamped hashlink to a record. Everything is a hash lookup this way and thus all nodes can store data.