BurrMan, Michael should of course answer that better than me, but I'll give it a shot:
MoI's UI is presented through a tiny web-browser. Just like any other browser it supports HTML/CSS/JavaScript. It's mainly through JavaScript that you can interface with it's internals.
Now I guess that Dave's app can communicate with MoI because it generates a popup window from within MoI's UI, so it's not actually a "different" app.
It's JavaScript (and some HTML/CSS) that's hosted inside MoI itself.
So I guess (and I could be wrong) that there's no way for a completely external app to communicate with MoI in an easy way.

The only thing I can come-up with, is that an app could be written in a specific way to make use of the clipboard, as a way to pass data from/to MoI.
That's the way MoI and Rhino can exchange data, but you can only do so much because you can't "affect" existing geometry this way.
Maybe another option would be to write an AutoHotkey script that target's MoI's window, but it depends on what you're trying to achieve for this to even be an option.