Thank you so much for the amazing and in depth answer. Literally my understanding of LE process just stepped up multiple folds. Thank you!
Certbot picked one of the existing overlapping certificates, essentially at random, and reissued that one with all of the names
Yup that seems to be exactly what happened because I was also confused about the certificate names, since it picked up one of the subdomains for the certificate name which you can see in my first post.