I do wonder if uncle is being intentionally written as aro ace or if it's more the curse of harem manga having to continually up the stakes while not confirming an end game ship until the very end.
You are reading too much in to it, Uncle is not aro ace or any of that, it's really fucking simple. He has never in his entire life conceived the possibility of a girl being interested in him.
Like that's the main gimmick of this series.
He was an ugly bullied autistic kid with no friends that not even His own family wants, to him the prospect of a girl liking him is nothing more than fantasy, he has no more reason to consider that it might actually happen to him than to consider that gravity may suddenly turn off tomorrow and he'll float into space, it's nonsense, it's unthinkable.
He's also not stupid or dense, since he picked up Fujimiya being in to Takafumi or that one girl having a crush on the commander almost immediately, He just doesn't think it could happen to him. That's why He won't react no matter how much the girls flirt with him.
It's also Why the elf's tsundere attitude in particular is bad for him, because he takes all the insult she throws at him literally without reading between the lines.
This is a real thing that happens irl to some people, obviously to a less extreme degree.
