Bundles have a colossal disadvantages. Change one thing and boom your user is re-downloading a pretty big bundle. Fine grained file resolution means apps can grow & evolve with very little user cost.
People harp on and on about the benefits of bundles for compression, but man, it's so shortsighted & stupid. It favors only the first-load situation. If your user actually comes back to your app, these advantages all go away, disappear. Personally I'd rather help people that use my app regularly.
Second, the days of bundles being better at compression are numbered. Work has been ongoing to figure out how to send compression dictionaries separately. With this, 98% of the compression advantage disappears out the window. https://github.com/WICG/compression-dictionary-transport
Neither of your approaches sounds like what I'd do. Personally I would build an http server that takes raw uncompressed source. When asked for a file the first time, it compresses & builds the dependency maps in parallel, & saves both of these out, maybe a .gz with some xattr on it. Or store that data in memory, whatever. The first user gets a couple extra ms hit, but the server transparently still does the thing. Developer mode is just a tool to watch the file system & clear those caches, nothing more, & can potentially be completely separate.
Bundles are just so awful. They complicate what used to be an elegant understandable clear world of computing. We can & should try to get back to resources, if it makes sense. And the cards are lining up to make this horrible un-web un-resourceful kludge potentially obsolete. I'm excited we might make the web make sense again for end-users. They deserve to be out of the bad times.
If it's calculated at runtime, it's an additional cost & delay, plus you'd need a specialized server (or at least middleware) to handle the requests.