It is fairly normal at a large school. Sometimes as an undergrad gains experience in the lab, they get more contact with the PI. Is he planning to research in the summer? He could consider applying for REUs to get some summer experience in a different lab (although I think the REU deadlines for this year are mostly past now). Or if this prof can’t give him research funding this summer, maybe he could try another lab. If he is applying for PhD programs, some require 3 recommendations. My kid really benefitted from having experience in 2 labs (one not really in her area for grad school — but still good research experience).
I’d suggest he set up time to talk with the PI in the fall. Tell the PI that he is thinking of applying to
PhD programs after graduating, and ask advice on the process. A PI helping with the process is huge, and it will pave the way for asking for recommendations fall of senior year as well. Be sure your son checks out the PI’s website (most STEM profs have one) for any info on grad school apps, recommendations, etc before meeting with them.