If he IS her father, then why would her mother never have told him so? It's not like she didn't have 9 months to tell him if it was his child or not, which means her mother was a 304 who slept around with other dudes, & the game's dev can take the easy, middle-ground by saying, "It MIGHT be Incest, or it might NOT be, since Amanda's mother was a 304 & never told MC who the father was, it's up to you -- the gamer -- to decide for yourself since I'm too spineless to say so; Enjoy suckers!"
Therefore, he MIGHT be her father, or he might NOT be her father. There's NO definitive answer! That's why it's a tease that flirts with the idea, but doesn't commit to it.