I have no words and think this is a front for some other issue he doesn’t want to talk about. I confronted him , but he insists that this is the only thing and his subconscious won’t let him be with someone short.

His subconscious? What? What the fuck.

He is either covering for another reason, or he is trying the timeworn technique of being a huge mean jerky idiot until you do the dirty work of dumping him.

Moreover, this is not how things work. It's not a one-to-one ratio "short mom = short kids."

My kid is in the 99th percentile for height and wears an adult size 6 shoe in elementary school.

Yet, I never grew above 5'2" and wore a size 13 kids' shoe in 7th grade. My dad was 5'6" and my mom 5'4", yet my brother is 5'9.