Never said Persona isn't part of MegaTen. It is. But MegaTen is a larger thing, and Shin Megami Tensei is part of that universe or franchise, just as Persona.
That means a SMT rep could happen without problem, because Joker only reps Persona, and his presence doesn't close the doors to Demi-fiend, Flynn or SMT V main character.
That's why I said Persona music isn't listed under "MegaTen series", because if that was the case that would mean Joker is considered as a rep for the whole Megami Tensei series, which includes more than Persona and SMT, and which by the way would have been a bad move unless they pulled off the SNK treatment and give us a ton of music or cameos from other MegaTen games beyond Persona.
TL:DR Joker is a Persona rep, not a MegaTen rep, if that was the case it would probably kill any chances for a SMT character in pass 2.