Hi Rob,
I have been studying this issue, gathering information from several sources (among which Apple's official documentation has been pretty useless), and it seems the problem comes from the way PixInsight declares support for several file types in its info.plist file (inside the core application bundle). For example, JPEG and TIFF files can be located without problems with Spotlight from a file dialog in PixInsight, but XISF and FITS files cannot. The obvious difference is that OS X knows well the .jpeg and .tif suffixes, while .xisf and .fit are sort of "alien" types and thus ignored. I'll try to get this problem fixed, now that I am on the right way (or so I hope...).