After looking at the code, I think the flag determining if MC is the father of Roxy's baby is backwards.
When the variable, roxy_i, is defined, it is set to 0 with a comment saying "impregnate Roxy." In the dialogue with pregnant Roxy, the bits of dialogue that seem match with MC being the father are shown if the roxy_i variable is NOT 1. However, in the first H scene with Roxy, finishing inside her sets the roxy_i variable to 1 and also in the season 2 new game onboarding section where it asks you your season 1 choices, if you say you finished inside Roxy it sets the variable to 1.
So yeah, I think the MC being the father or not is actually bugged right now.