“his math teachers are supportive of this advanced path”
This might be key. If the teacher is the sort willing to work with him, as needed, and he’s able to ask for support (self advocate,) it can make a difference. In turn, that can include a fine LoR.
There’s nothing wrong with an “eyes wide open” approach, as long as it’s balanced.
This isn’t about Stanford, per se. It’s a combo, imo, of him looking ahead but not knowing his future college options and wanting to challenge himself. Many younger kids focus on a sibling’s school, not knowing other names.
You can always suggest other fine, large universities- casually introduce them. Imo, it might be early to advocate swapping what he (thinks he) sees in S for a small LAC. There’s time for that later, lots of growth yet to occur.