Would this not be solvable by just making it all arbitary WASM code? As long as the simple WASM sandbox is secure, it doesn't matter how buggy your internal SQLite implementation is.
This article only contains mostly information on adding more limits to avoid DoS—nothing there would harden WebSQL against SQLite vulnerabilities except for SQLITE_DBCONFIG_DEFENSIVE, which was only added in response to the zero-day bugs that were found in Chrome after implementing SQLite.