If you're using Webpack is it possible to gradually opt files into TS type checking _without_ having to rename them, since you can specify which filename patterns loaders apply to?
It might be worth checking ts-loader or awesome-typescript-loader. I'm not sure how it detects js vs ts in those pipelines. TypeScript can also "compile" JS to check for syntax and other errors, so it may still be extension based. An interesting scenario though.
I believe you might be able to with --allowJs, but to be quite honest I haven't done so. All my projects were TypeScript-based from the start, even if sometimes I end up using JS dependencies.