Then why can't the new files just be inserted by the package manager?
In theory they can, that's what these binary diff programs accomplish. I mean, you can't JUST insert data in the middle of either a squashFS or ISO, you need to also manipulate the entry table at the start, but it's not an impossible task, binary diff tools take care of that as well.
But again, all this requires work. Milkshake and B-ZaR (and anyone else who wanted in on that committee) would need to discuss a communication standard for sending updates, how to store and apply the diffs, Milkshake would need to update the server's code to create these package diffs and B-ZaR would need to update PNDManager to apply them, and EvilDragon would need to agree to the increased CPU usage and extra storage required.