You are correct, it does copy the files locally. There are several reasons for this decision (and it was not an easy decision to make). Handling files this way simplifies things in many respects. There’s no dealing with files having been removed from the photos library, and many files would have had to be stored locally in any event (when sourced from somewhere other than the photo library).

In the long term there will be more focus to bypass the iPad photo library entirely. Importing wirelessly directly from devices such as eye-fi, for example is one way to eliminate that need. I also hope that Apple will open up access to the camera connection kit to allow developers to import photos directly.

Filterstorm Pro does not yet sync with Aperture or Lightroom, but this is something I plan to begin work on after Filterstorm 3 is complete.
Tiny link: http://taii.cc/56