Those things are probably stored in the database. I don’t believe Trellis includes anything for automated database transfer because reconciling WordPress databases automatically is a hairy problem that AFAIK has not been solved. Generally your options are:
- Manually copy-and-paste over any changes
- Push your entire database, overwriting whatever database exists on the remote server
- Manually resolve database differences in the database itself (which sounds like a nightmare)
I use WP DB Migrate Pro, which is a great plugin, but keep in mind that it is overwriting your databases, not combining them.