It doesn’t matter if that timeline no longer exists. Or if one of them was really inside a remote controlled robot at the time. The Doctor and River consider themselves to be husband and wife. That is all that matters.
River Song was conceived in the TARDIS which altered her DNA. She is kidnapped as a baby by the Silence and experimented on to make her half Time Lord. All of this allows her to communicate with TARDIS on some level and learn to pilot the craft with skill.
River is quite proud of the fact she can fly the TARDIS better than the Doctor, someone who never bothered to read the manual, failed his test, rarely ever gets to where he wants to go and yet still acts like he’s the greatest TARDIS pilot who ever lived.
So of course because River is better at someone than the Doctor she is called smug, a Mary Sue and hated on by a vocal minority who arrogantly think they speak for the entire fandom.