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Looks like you can just specify the port in the dbhost field in config.php, as mentioned in #632 (comment), so say your custom port is 1234, you'd do that in values.yaml like this:

 externalDatabase: 
   host: "myhostname.com:1234"

We'll look into updating our docs to reflect that as soon as we can :) (here's the merged PR for more doc: #634 now available in 6.0.2)

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