In that case, which URL will be showing in the browser, Atlassian URL or custom URL.
If you get all your rewrites correct, it'll be the custom one. Until they click on something you haven't rewritten.
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You could do something with proxying, rewrites and so-on if you're running the server behind the custom url, but the Service Desk will still be running on the Atlassian urls, and people will silently end up using the Atlassian url in the end. (Especially if you use email, as that will always be the Atlassian url)
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