How to force iOS apps to use global proxy settings
I was able to proxy URL requests from 4 apps I just tested (Instagram, App Store, Omni Focus, Bookmarks). I used a manual proxy configuration and Charles to test.

I'm not sure what proxy API you're talking about. From personal experience, I know that any app using an NSURLConnection to make the request will go through the proxy as defined by the system. It's possible some apps use a socket directly to make the request - if so that may bypass the system's proxy settings, but I'm not sure about that.