Zero (and I believe Replicache as well) layer their own SQL-like semantics on top of an arbitrary KV store, much like the layering of SQLite-over-IndexedDB discussed; like SQLite-over-IndexedDB, I believe they are storing binary byte pages in the underlying KV store and each page contains data for one-or-more Replicache/Zero records. The big difference between SQLite-over-IndexedDB and Zero-over-IndexedDB is that Zero is written with sympathy to IndexedDB's performance characteristics, whereas SQLite is written with sympathy to conventional filesystem performance.
On the subject of "keep whole thing in memory", this is what Zero does for its instant performance, and why they suggest limiting your working set / data desired at app boot to ~40MB, although I can't find a reference for this. Zero is smart though and will pick the 40MB for you though. Hopefully Zero folks come by and corrects me if I'm wrong.