This is exactly what will happen.

Diff the same video a few times and you’ll be able to figure out which is injected content and which isn’t.

Separate out the injected content and you can fingerprint that content like how Plex or Emby fingerprints intros to TV shows (i.e. it’s a solved and known problem).

Then you can reliably identify the injected and content, you know how long it is and can just tell the client to skip it.

This won’t be easy, it’ll require more than folks indexing ad content but it’s feasible.