IMHO, the Captain was feeling justified in marginalising Anne. He had the indignation of being refused all those years ago, and has a rigid temperament, so cannot easily forgive.

So he was being sort of "cruel" if you like, on purpose, to show her his offence and his indignation. The faith he had in himself, the promise to succeed and become successful and wealthy, ought to have been believed in by Anne.

In some ways, I would venture to say he puts her in the spinster role, by saying the seat was hers, rather than inviting her into his company.

I could be wrong but I get a nuance that he is thinking Anne's position is her own fault for not believing in him. What is interesting about this is that he uses "studied politeness" to hide the indignation he feels underneath.