Geez he really is a rebel against nobles huh. Even he knows he can't leave her behind but he also can't sacrifice his crew's freedom as well. Maybe sometime he'll get a situation where he can have a little power with the nobles THEN he'll accept her.
I think this is not explained enough, but Mei's behavior is also out of fear, not just loneliness.
Considering crystal lifeforms can assimilate machinery and turn them into their kind, it's the equivalent of fighting an armored zombie virus to machines. Of course it'll instill fear to machine...
She has unconsciously accepted her fluttering feelings and reflexively danced it away to resonate with him. No matter how awkward it’s certainly the primordial form of romance.
It really was pretty difficult to stomach reading all that but it was a very satisfying read. Dealing with problematic children with power requires power. Adult power that even that spoiled brat can't take on his own hands.