So I have been replaying FS2 under Knossos with the latest media VPs. I was playing the final mission and forgot exactly when the supernova began and was too far out. I was racing for the node as fast as I could (flying an Ares) and heard the wave approaching. I used my hat switch to look aside to see it and it came up on me and I got the external 'you're dying' image, but as the counter hit zero I was suddenly returned to my cockpit, and my ship was fine, as were all of the rest of the surviving ships. I watched as they all reached the node and departed. Command announced as each one (save the two surviving Lambda transports) departed safely. When I jumped out I still ended up with the 'Alpha 1 is dead' cutscene following the supernova one though.