The difference between GPS altitude and FL is one of the issues causing problems in the creation of a truly unified collision avoidance system. FLARM uses GPS altitude to both avoid collisions with other FLARM equipped aircraft and obstacles on the ground. Most other systems use Mode C, or a sensor calibrated to 1013, to calculate vertical separation. FLARM (despite being uncertified) appears to work well in Europe, but I have always been sceptical that the two systems could be brought together in one box. The people developing the systems have always clamed there was no problem, but I have not got my hands on one to test it yet!
Rod1