Mysql – Why does the MySQL command line tool ignore the –port parameter

Please note the --skip-networking parameter

Yes, very likely the cause of the issue. Remove skip-networking and add "bind-address=127.0.0.1" instead in my.cnf.

I guess java connects via network only and does not use socket connections, which is what you do with mysql cli tools.

You're doing your ssh forwarding backwards, i.e. you're forwarding local port 3306 to 33187, use -R localhost:33187:server.domain.com:3306. For the workbench use MySQL Server Port 3306 and MySQL Hostname: localhost

What specifically is the error you're getting, I'm having a problem myself using a custom ssh port, i.e. SSH Hostname server.mydomain.com:13711 the workbench for whatever reason doesn't actually attempt a connection (verified by watching the logs)