What would be the best practice within AppConfig for enforcing the case I described initially - that is, CLI args are loaded at script startup and preserved throughout execution despite reloading from the config file with each lifecycle of the daemon?

I imagine do whatever makes sense to you, and document it

Take a look at the defaults of Daemon::Generic, you could (in your subclass) inject a --preserveargv or --discardargv option ...

Document whatever you choose, documentation is key