How can I open an application URL?
Maybe I don't get the question right but:

You may open such an application URL in almost any available application with text fields or text boxes: highlight the URL (sometimes even only parts of it - at least the scheme and the first character after the :// (e.g. airmail://m - are sufficient to open the application), right-click and choose "Open URL". And yes, it's of course also working in the Chrome/Safari Omnibar: Just enter the URL and hit the "Enter" key.

In Evernote you have even two ways to open it: 


You may paste the URL(s) in a note and by choosing the whole URL or parts of it the context menu offers "Open URL"
If you have only one application URL in your note, you may add the URL to the "Note info" (red circle) and then you'll get a clickable link with the "scheme specific part" of the URL or only parts of the "scheme specific part" - here "message" (blue circle). 




In the Terminal you have several ways to open the URL:


highlight the whole URL or parts of it and the context menu offers "Open URL"
highlight the whole URL and command &amp; double click it
enter open URL
(e.g. open airmail://message?mail=myAccount&amp;messageid=etPan.55ba060a....)
(OK, the interaction between Terminal and Airmail2 uncovers a glitch, because Airmail2 opens if closed, gets to the front and the message is chosen, but the GUI is not visible.)