Car companies don't tend to custom-design knobs/buttons/etc. for each model. They tend to reuse the same ones across many models to save on development and manufacturing costs. They also already modularize these knobs and buttons across different "accessory classes". You can probably see this in your own car even, if you see anywhere on your car's center console or dashboard which has plastic caps where it seems like more buttons or knobs belong. Those are likely buttons/knobs for additional functions in optional feature packages.

Also, even for the same screen size across models, you'd still likely need custom bezels since most models are differently sized and thus have different dashboard shapes/sizes within which the screen is mounted.

Especially with how high-resolution touchscreens in cars are becoming in new models, I doubt they're cheaper than a handful of plastic knobs and buttons.

My guess is that it's exactly what they said. It's probably harder from a software perspective to adapt touch-screen-based interfaces like Android Auto and Apple Car Play to physical controls, and those difficulties probably come up over and over as the versions of these interfaces on the phones are constantly being updated, and the car must continue supporting more and more versions at one time.