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My workaround for supporting scripts and modules is to essentially trick it.
either specify the source and script source with the fqdn version of the url and then a shortversion of the url or, what I do, set up a iis front end for redirect urls.
i.e. if your server name was repos and your domain was mycompany.com then you might set source to repos.mycompany.com:8624/nuget/myrepo and set script source to repos:8624/nuget/myrepo
You can list and publish scripts or modules to the same repo and find-script will differentiate from within the repo.
The more elegant solution, but more difficult, is to create a dummy website with real or virtual paths that use http redirects to the right sight. So you could set your source to something like repos.mycompany.com/source and that folder would redirect to the path on the different port.
That's just a quick summary of the workaround, I realize that, I can provide more thorough examples if you would like.