I dont think its for mike, BUT "Far From Heaven" is, I think. Listen to the lyrics and remember it was james who wrote it. I think its about Mike wanting him out of the band. You can imagine it is hard when the leader of the band want you to be replaced.
Far From Heaven is not about Mike. James has said that it is about the hopes and dreams people put on their children wanting them to be something they are not. They definitely fit that.
Now as for "Beneath the Surface" personally I thought that was a possible interpretation of it. It is written very broadly and can apply to many different situations. This is definitely my favorite kind of lyric because it has a stronger chance that more people can relate it to their personal lives.
But if John said that isn't what it is about I'll take his word for it. But I don't think people that think this has to do with MP are really "digging for nuggets". That is a plausible interpretation of the lyrics. Now the people on page 5 or 6 of the review thread that tried to tie each single line in "Breaking All Illusions" to different Dream Theater songs: THAT is digging for nuggets.