You are confusing SSL and HTTPS. Port 443 is the default port for HTTPS connections. MySQL uses 3306 instead (and can use SSL over this port or any other to encrypt the connection). So, setting up SSL encryption for a MySQL connection doesn't affect the used port.
In order to use a different than the standard port you have to reconfigure the MySQL server, which you probably cannot do with an RDS instance.
It is possible to use tunneling to avoid the default port. In this scenario you have to open an SSH tunnel (MySQL Workbench can do that for you or you use an external program like putty on Windows or ssh on *nix like OSes). With that tunnel in place (which uses port 22 by default but can be configured for any other port if that matters for you) you can then forward access from a local port (here 3306, but can be any) to a remote port (can be any as well). This requires an SSH server on the remote end however.