From the docs:
While i have never tried it, it might be worth a shot at passing the custom port with the option above. Just use standard hostname:port naming. ex. mydatabasehost.com:2605
Whether this works or not, please respond back here. If it does then we can make a note in the title of the thread so that future searches find this answer. And for the inverse as well.
Just to elaborate on the above comment.
ee site crate example.com --type=wp --dbhost=mydbhost.com:6606 --dbuser=youruser --dbpass=yourdbpass --dbname=yourdbname
And for any site with an existing db that you move to a managed db, all you have to do is change the wp-config.php file for the site and set the database as per the Wordpress docs as mentioned here https://wordpress.org/support/article/editing-wp-config-php/#set-database-host