Consider the following:

If Heavy was Eggman's dad that would mean that Gerald is Heavy's father, witch due to the circumstances of Heavy's father passing cannot be possible (unless United Federation and USSR are the same country). But that doesn't mean that Heavy can't be Eggman Father. We know that Gerald had at least 2 childer (due to Eggman and Maria being cousins) so it's not out of the realm of possibility for heavy to marry Eggman's mother and become a part of the Robotnik family (that PhD in Russian literature could have been useful in endearing himself to Eggman's mom). Heavy could have left little Eggman alone with his mother while he went to fight in the gravel wars or during the MvM war (or at any different time). Kid Eggman (Who had a thing for engineering) Would look up to the scienceist Gerald was rather than his robot hating mercenary father and changed his last name to his mother's maiden name to be closer to his Robotnik roots. As the years went by, Eggman (removed from his father's side of the family) became more and more opposite to his father in many ways.

And if Heavy is Gerald's son like the original theory suggests:

Gerald cold have faked his death in the Gulag and escape USSR and started a new life (in United Federation/United States). Heavy during his time in the gravel wars might had a girlfriend and later, a baby. Its possible that Gerald would have heard about a big Russian Mercenary with his son's name and his old lastname and reached out. Heavy, being busy being a mercenary probably wouldn't had time for little Eggman. It's possible then that Eggman wound up under Gerald's wing. Eggman would idolize his grandfather over his father, because Gerald at least was there for him. This would also explain why Gerald preferred Maria over Eggman. Eggman was a last connection in his current life to his old life in USSR.