I think they used the extra vote. They knew Thomas went on a journey and lied about it, so they used the extra vote to pad the votes against him just in case he had/used a steal or block.

The only people up for elimination at that point were Sai and Justin (due to the deadlock vote and Mary as Safe). Because those are the only people, Sai cannot vote for herself, therefore she could only vote Justin.

No, she gave up her vote