I highly doubt we get any incest of any kind. I think this could be about MC's mother being related to any of the preps in some way.
The MC could for all that we know so far a cousin of thud ... tad .... thadeus tentacle.
But that would not explain why father stresses the importance of condoms every time it comes up even remotely.
Judging by fathers personality that would mean he wants to protect his son from an error he himself made and not "a normal father son talk".
Come to think of it an STD would also be possible. If he contracted it unknowingly before meeting mom, infecting her and due to the pregnancy she was unable or unwilling to get treated.
Actually that makes somehow more sense than father being a father to another offspring.