Actually that's exactly what it means.
A game is much more than the scripts built on top of it's engine. Take away that engine, and you have nothing. Take away the scripts, and you have nothing too. Neither can take full credit for the whole of the game, so you can't rightfully say the game (as a whole) was written in Python, just as I can't say the game (as a whole) was written in C++.
This demonstrates your flaw of logic perfectly:
While I'm perfectly aware that the underlying engine ([...]) is written in C++, the actual games ([...]) are written in Python
You can say we're arguing over semantics, but in your own words: I think you have a serious misconception of what constitutes an actual game.
The engine that runs a game is every bit a part of the actual game, as your car engine is a part of your actual car.
Just because it's "under the hood" doesn't mean it's not there, and that you can pretend it doesn't exist, or doesn't matter, or is any less important to the "actual game" or "actual car".
Saying that a game's Python scripts are what makes the "actual" game is like saying your car's steering wheel and dashboard is the "actual" car.