An App Proxy returns a string. Call it Liquid. Shopify then renders it. If you just use an App, and it returns a string, you can simply insert the string in the DOM and achieve the exact same thing. In fact, in my travels with App Proxy, I have often wondered why I bother since I can almost just as easily use a plain jane App to same affect. I get the comfort of Liquid in the Proxy though, and since you can hot-rod your own Liquid in your App to do so much, it is convenient. Maybe you can use the ONE App Proxy, but supplement your other need(s) with App only processing?
One thing I suggested about the App Proxy that would in fact get me using it a lot more would be if it would allow you to skip the layout. That way the Proxy Liquid could simply replace the sandwich filling we call "processed data" and leave the bread alone. That would really step it up for me, but alas, still waiting on that one :)