MySql not using Buffer Pool
Fool that I am... the server was restarted this morning. I realized this as I was finishing the question. The buffer pool won't fill up until the database actually needs to use that much data. Indeed, if I re-run the buffer pool query I can see the "Free buffers" number slowly decrease.

I could run some queries to force tables into memory, but given I know I don't have enough memory to go around (hope to address this soon) I should just wait and let my users tell the DB what data is more important.