Can APT take a single flat image in order to attach hotspots and not warp the image into a pano? For example Garden Gnome software can specify a flat image on file input and preserve the flat file throughout the hotspot additions.
You certainly can in V1.1.0 beta 7. After you import the photo, go to 'Panorama Properties' and select the planar output projection option rather than the default spherical one. Then add your point or rectangle hotspots.