"Did his dick suffer a grave incident" Yeah, cause his dick got buried 6 ft deep in that architect-slash- mad technician pussy. /JOKING

Alhaitham has more internal cybernetics installed, the only things he has visible are his headphones that act as hearing aids and a communication tool, he also has a device connected to his chest area which is also connected to his heart. All of his installations are internal but he does keep more of his human parts (penis included but with a twist!) In comparison to Kaveh who had to suffer a great loss at first but managed to recover thanks to his cybernetics and modeling his own prosthetics.

Alhaitham is able to "modify" his dick the same way he's able to modify certain parts of himself (durability, temperature, and such. Yet they all haveimits due to the fact Alhaitham isn't 100% metal plating therefore he has to be considerate of his own limits and not rely fully on the personally installed cybernetics that assist him in his research and connecting more to his own tech. It's why despite having access to the internet directly to his brain, he prefers physical books.)

Alhaitham is able to produce his own sperm (and naturally, more!) And he's able to wear a "prosthetic" (like something around his dick) for further stimulation with Kaveh BUT Alhaitham prefers to go all out with just his own dick cause he likes to feel flesh with flesh- especially Kaveh considering he only has his face, Fingers, and rear region being his remaining flesh.