The reversed coordinate system is "the way it is supposed to be" from what I've seen on the mailing lists, it's not considered a bug and no "fixes" will be accepted for it, so consider it a corner case
People may want to try to decompress their roms before they run virtual jaguar, as sometimes Mac OS X will hide the .gz extension and that will not allow the file to be recognized (maybe we should parse for .gz?). Static linking is necessary on OS X because, like Em said, it's not really acceptable to have people install libs before they use it on the Mac side.