Um, if it’s “parallel” (e.g. separate from the OS package manager) then it’s not centrally managed. The OS package manager is the central management.
There might be specific use cases where this makes sense, but frankly if segregating an app from the OS is a requirement then it should be fully containerized with something like Docker, or run in an independent VM.
If a flatpack is made reasonably, then it gets library updates independent of the app developer doing it.
That feels like a load-bearing “if”. I never have to worry about this with the package manager.