This is a really great point. I think something like a `.svelte.js` file extension is warranted here. This would key tooling to when it needs to interpret runes, and makes it clear which files in a codebase require the svelte compiler. These files clearly aren't just js/ts at this point, but I think its fine as long as they're marked as such. Custom react hooks, for instance, aren't usable outside of the runtime but can be transpiled without issues by esbuild/tsc and interpreted correctly by a js/ts language server.
As long as it's marked separately from js/ts I don't think its a huge issue though. Svelte files already have script tags that aren't completely vanilla js/ts.
Ironically typescript doesn't have a supported language server from MS. TSServer (in the typescript npm package) is language server-esque and that's what VS Code plugs into. I believe the main language server for typescript is maintained by sourcegraph.
VS Code is written in typescript though and the projects have a pretty nice cadence of new features. Typescript is very much a first class citizen in VS Code
As long as it's marked separately from js/ts I don't think its a huge issue though. Svelte files already have script tags that aren't completely vanilla js/ts.