This article is kind of a messy read, isolated declarations feels like it's being used as a mcguffin to advertise the jsr registry. Both may be neat things on their own, but I feel the connection is a bit misleading.
Isolated declarations should allow parallelization and faster type checking with tooling that supports it. This shouldn't be changing your build/release process or what you export in your package.json.
If you also happen to use the jsr registry to publish your package, it sounds like you can update your package.json to export TS files and they'll compile/inject the JS into your release artifacts on publish. Not sure if this feature requires isolated declarations though.