The PRT Loader supports loading multiple sequences of files in one object. It also supports tagging each sequence as visible in the viewport, at render time, or both. Typically people will add a proxy sequence tagged to only load in viewport and the render sequence to only load at render time. You can check out the details here: http://www.thinkboxsoftware.com/krak-prt-loader/#Viewport_and_Render_Controls.
The PRT Loaders don’t do anything fancy with instancing. If the same sequence is present in multiple loaders, the sequence will be fetched from source multiple times. It might end up caching it for the viewport if you use actual node instances but it will not do this at render time.
Not what I expected. I think this might be caused by dropping the viewport cache before rendering and needing to reload it from source afterwards, while the instanced PRT Loaders have special (read: annoying) viewport behavior that allows them to keep the cache. Nevertheless more caching controls are a common request and are on the wishlist.