> WebSQL would have been tied to one specific version of SQLite, and developers would have to work to the lowest supported version. There would have been no extension mechanism.
Why not? Web SQL would not be different from WebGL/GLSL or even JavaScript itself in that respect. Developers use feature detection and and work to the lowest supported version. APIs and languages can evolve, but in (mostly) backwards compatible ways. Extension and versioning mechanisms can be made. That's how the web works and Web SQL could have worked that way too.
More broadly, you could apply arguments like this against everything in the entire web platform. Maybe everything should be a WASM module that developers could choose themselves! Image loading, video decoding, font rendering, DOM, JS engine, why not? It's actually a beautiful vision and I'd be all for it if not for cache partitioning. Every site would have to re-download and re-JIT an entire browser engine before it could do anything.
The base platform needs to include a diverse set of commonly used features so that apps don't have to download the world, and on a list of ubiquitous libraries SQLite is right up there with other libraries backing the web platform, like zlib.