There are two kind of properties, Custom Properties for the JS API/Mail Apps, and UserProperties for the VSTO/Object Model (.NET).
I know you can't access Custom Properties with the Object Model because they're basically data for the Mail App itself (storage). However, it would makes sense if the Mail App could access the UserProperties with the JS API (as these properties are bound to an item, like mail or an appointment). Is this possible at all?
So far I've only found this:
However, these two custom properties are different and not interchangeable. That is, we can’t get one type of custom properties from another.
http://sharepoint1488.rssing.com/chan-6873411/all_p1.html#DiffPlatforms
I can't immediately find anything in the JS API library, so I'm guessing I already answered my own question, but I want to make sure (as it seems odd to me).
It's not possible via the JS, but you can make EWS requests from the backend to get the entire item. you can read any property on the item from there, so long as it is saved to exchange.