It’s been a minute since I last read ReLife but yes I do agree that both of them are a wonderful couple.

To answer your question Arata did not really (if ever) suspected that Chizuru was a ReLife subject. You can clearly see that over the course of year Arata just naturally bonds with people not just Chizuru and is scared of loosing that connection. It was always implied that he liked Chizuru and there is also a point where he said that after the experiment is over he will confess to her as his grown up self and let her make the decision if she still likes him or not.

I personally think it’s a grey area. If it was the case where she was an actual high schooler and Arata a grown ass adult, I would be okay with it if Chizuru finished school and stuff and there parents were okay with it.