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Bloomberg's comdb2 does something similar, using the SQL grammar and query planner but swapping out the storage layer. To quote from their paper:

"In SQLite a query plan is compiled into a bytecode program that is executed by a virtual machine, named Virtual DataBase En-gine (VDBE)... In the original SQLite implementation the VDBE operates on the real B-trees of the database... In contrast the Comdb2 VDBE operates on the cdb2 abstraction of a table during the OCC phase of transaction execution..."

http://www.vldb.org/pvldb/vol9/p1377-scotti.pdf

My guess would be the b-tree layer down based on "the database backend module that it uses to store b-tree structures in its database file" and the architecture diagram at https://www.sqlite.org/arch.html

This feels to me a little bit similar to MyISAM v.s. InnoDB in MySQL - two different "backends" that are low level details about how the data is actually stored and accessed.

> How much of it is still SQLite at that point?

I'm guessing just the interface. If there are any well-understood quirks of the regular implementation, maybe they'd want to replicate them too, idk.