X-plane is working on Rift support as we speak. FSX works with the Rift now if you use TriDef driver. However, I can confirm that the problem with lights/PAPI rendering as a 2D overlay is there. It doesn't matter though, it's totally worth it to fly with the Rift! EVEN if the resolution is so crappy you can't read the digits on the instruments. And EVEN if th lights are 2D. Just fly in daylight. It's that awesome! I didn't believe it myself, before i tried.
And to you who have yet to meet someone who hasn't gotten headaches and eyestrain after less than 40 minutes: I never had any problems whatsoever. No nausea, no headache, no eyestrain. And I've played for eight hours straight. I guess it varies from person to person.