I saw in the release notes for Xcode 15.4 that something like this has been addressed - (116698465) (FB13253099)
At least in my use case the problem seems to have been resolved. I am using SwiftData for managing persistence.
Use Case
download a container.
Manipulate the SQLite database
Replace the container.
The changes that I have made are visible in the app.
This previously failed
Xcode - 15.4
MacOS - Sonoma 14.5
iOS - 17.5.1