For at least the Nintendo Switch (not sure other modern conosles), the digital distribution infrastructure is built in terms of overlay packfiles. Games, updates, and DLC on disk are all single-file archives / filesystem images. The OS, when launching a game, mounts the game + its updates + its DLCs together as a transparent overlay filesystem. The game just sees a unified representation of its newest version, with whatever DLC has been installed, sitting under (IIIRC) /title.

I wouldn't be surprised if the other consoles also do things this way. It's a very sensible way to manage updates — especially when a game is running off of physical media but the updates are held in local storage. It also means there's no point where the update gets "merged in" to the base image, which means updates can be an atomic thing — either you have the whole update file downloaded + sig-checked (and thus it gets added to the overlay-list at boot) or you don't.

And, if all the consoles are doing it, I wouldn't be surprised if studios that do a lot of work on console don't just use that update strategy even on PC, for uniformity of QA, rather than for "obfuscation."