Data is stored relationally in Postgres in 3NF. References are indexed automatically, but you still need to index type properties if you use them in `filter`.
FWIW, I do think there's a space in the market for a thin wrapper over Postgres (or MySQL) which would automate certain optimisations such as whether to index a particular table. It always struck me as perverse that that optimisation was delegated to the developer, when it's no more subjective or application-specific than a thousand other automated optimisations the engine makes. I'd be really interested if your project covered that.
There are countless permutations of the choices that database designers face, so it's a shame there aren't mature products for more of them. I hope this particular permutation turns out to be a good one for lots of people :)
And you - or hypothetically the end user - could change the backend, e.g. to Cockroach for better horizontal scalability, while trusting that EdgeDB will only rely on Postgres's public API at least in meeting its own public API/contract?
[0] It's hard to make that analogy with Postgres b/c it only has one storage engine, but of course the separation still exists.