If, on a empty train, someone came and sat next to me rather than an empty bay or table I'd, if I was going to be on the train any length of time either ask them to move or move myself, depending on the circumstances.
It'd at best come across as strange, at worst provocative or threatening behaviour to me. Akin to the strange person on the bus you don't want to be next to, or the person in a pub looking for a fight with a lone stranger.
Of course they might not be threatening at all, they may just have, what I'd consider, an over concern with rules, or be autistic, and be perfectly pleasant. I still don't want to sit next to them though.