I find it weird that considering the boost appears to be enabled at a OS/base level, why does it not boost the system overall, in-turn boosting all games - including games that have a 'pro update'. So the mode specifically targets games that haven't had pro-updates?
The key to understanding this kind of thing is always to work backwards until you get to the basics, once you understand what Boost Mode does it'll be obvious why it doesn't work with pro compatible games.
Normally, a PS4 pro runs at full speed playing a game that knows its on a PS4 pro, but when you play an old PS4 game on a Pro the game never says "Hey I'm running on a pro" and so the console throttles itself back to the performance of an original PS4 just to make sure everything's gonna be OK.
Now, with boost mode, you can tell the PS4 Pro to never throttle itself even when it doesn't get the message that the game is PS4 pro compatible. This results in older games running better but could also mean some games have issues where they are expecting a PS4 and not a PS4 Pro.
That's why it's a use at your own risk feature, and why it works in the games it does.
