Right. I totally agree with your outline. The Behavior for example on Webkit Apps or Google Chrome Apps is, that the WebApp allows Tabs, where target="_blank">Link 2 (FileToEdit)</a> opens then as Tab within the same Web App.
I had somehow the same exceptions, as Mozilla, Chrome handles it within a Web App, because on certain circumstances, lets say you are in a file directory / dms or in a crm application, specific links are with purpose coded like this, in the example of share/dms, you keep track on the folder structure in tab0 and on tab1 you can edit this file..
I suggest, a setting for the handler in the Web App would be easy to implement, and solve a general issue, user can decide how they like to get it handled. I also would spin this wheel even further, where you can restrict that behavior based on your choice, to a list of Domains/Sub Domains. And everything else, opens in Default Browser (which is hopefully soon on all Desktops set as Default Browser)...
With such a feature built-in, Orion becomes a Browser for Productive Work too, where users tend to make an Web App for it. Just an Idea, and Thank you for your quick detailed answer. Its often a small detail, which makes an Application to a Killer App and accelerates user adoption across different application scenarios.