"By that reasoning, if you have one package on your system that's not managed by the package manager, you should discard the package manager entirely."
No?
Something like "I want to play TF2, so I should update Steam and TF2" is a reasonably common thing and it makes sense to want one thing to handle both of them.
"You should discard the package manager entirely" does not follow from that.
You don't need to update Steam to play TF2 any more than you need to update Gnome to play TF2. By your reasoning, if you should need to update Steam to play TF2, and therefore need to keep Steam out of the package manager, you should also update Gnome, and therefore keep it out of the package manager, as well as the kernel, and pretty much every other package, just to play TF2.
Ergo, "you should discard the package manager entirely".
Steam is separate from the games, it's just an installer. You can play (and update) the games without the installer, therefore at least Steam should be a managed package.
"and therefore keep it out of the package manager"
That is not much like my reasoning. Taking something out of the package manager does not generally make it so that it is taken care of by the same thing that takes care of TF2 being up to date. Making Steam handle Steam updates does.
Once you have introduced Steam as a thing that handles updates for you, moving Steam updates from package manager to Steam is clearly not exactly the same issue as removing things from the package manager in general.
(I mean, it sort of is if "the package manager should handle as many things as possible" is your goal. It is not if "as few things as possible should handle package manager-like things" is your goal.)
The more packages managed by the system, the better. Ideally, you'd want the games, too, but I understand why Valve might not like that.
Using the unclean alternative when there's a clean one that's just as good isn't a good decision, in my opinion.