I'm not a Replay Gain expert either, I only really started using it a few months ago. It is kind of confusing. Hopefully I can explain correctly.
a)Because of the production and mastering techniques used on most commercial CDs, their loudness is very close to or above the limit where clipping of the audio signal occurs. The official Replay Gain specs (which is what MJ follows) use 83dB as the target loudness, which is 17dB lower than the maximum before clipping. Note that developers of other Replay Gain tools like MP3gain, Replay Gain (for MPC) and Vorbis Gain use 89dB as the target instead of (the official) 83dB. This was to appease people who complained that 83dB was to low, especially when listening to portable players. So, if you us 6dB in your Global Settings, this effectively raises the loudness of the files you analyzed with MJ to 89db and just gives you a little extra loudness boost. You can choose any value you prefer for the global setting,though. It has a range of /-12dB, I believe.
b)The Replay Gain feature in MJ works with any format that MJ can play.
c)AFAIU, the Replay Gain anaylization in MJ only affects playback. If you want to burn a playlist that has been Replay Gained in MJ, you must first playback the list using the Disk Writer plug-in, which will write new Replay Gained wav files to your hard drive and then you would burn using those wavs.
Rob