Yes. And?That's all fine and good, but that definitely is the players affecting the stakes via means their characters are not aware of.
In D&D play, players set the stakes by means that their characters are not aware of - eg someone might say "This new WotC module looks cool", or the GM might say "Who wants a campaign about fighting Kobolds and their dragon overlords?"
It's natural, in a game that involves creating a shared fiction, that participants in the game will shape what the game is about in all sorts of ways, both formal and informal.
EDIT: here's another example, from D&D.
Suppose that the PCs all build their PCs who are LG or NG. It would be very atypical for the GM to then frame the PCs into an adventure that is designed to proceed on the basis that the players will kill and/or torture a whole lot of villagers.
But obviously the PCs aren't deciding, via their moral and religious convictions, what sorts of challenges they are confronted by.