But the TV comes with the remote. An appliance with an app doesn't even have the courtesy of a remote.

It's somewhat the same problem because its possible to lose manufacturer remotes.

And if the TV decided to implement weird, non-standard control signals, it can be a pain to access certain functionality with universal remotes (e.g. settings).

Different path to get there, but same end result: not being able to access functionality without going through an annoying manufacturer-specific route.