Very true, I just rolled out annotations for Kavita (a self-hosted book/comic server) and epub doesn't have the ability to store it in the file (although Kavita has a no-modification policy).
Although for cases like Kavita, storing in the file would be problematic if multiple users want their own annotations without concerns of data leaking.
Although for cases like Kavita, storing in the file would be problematic if multiple users want their own annotations without concerns of data leaking.