I'm one of the primary advocates of "best albums get more songs in the finals", and while I understand the additional burden of having 30+ songs in the finals, not all albums are equal. The finals should have the best songs, not literally only the two best songs off every album. At the World Cup you don't have the same number of teams from Europe, Africa and Oceania.
But still this is all good fun and there is no "best" way to run this, and I appreciate the effort of each and everyone's host of these survivors. Probably the rules should be tailor-made in consideration of each discography, take for example Yes who have 3 songs on their Close to the Edge album, that kinda throws the "best 2 songs of each album" thing into disarray.
And a minor nitpick about "a song that finishes 3rd in its album survivor doesn't win the finals" - with such a tight album as this, it's not out of this world for my personal favorite, Creeping Death, to arrive third losing of a single vote to, say, Bells and Fade, but to eventually win it all because Bells and Fade lose to Master of Puppets or Sanitarum. Rare occasion however, I know.