More MySQL port fixes.

There were still some places where this wasn't working with MySQL on a different port. This should fix that.

There's also a commit in here for 'amp create' to use a new option I added so that it can prompt the user and still capture the environment variables. This goes along with a pull request I just did for amp.

This also needs a change to civicrm-core/bin/setup.sh which I'll make another pull request for.