In a basic, competitive game, is there any other significance to the stages (white lines) on the shadow track other than lair cost?
Hmm, I think you listed all the rules. The only other thing I can think of is some villains have an ability that triggers when the Track enters a new stage. It doesn't matter what stage, just that the marker crosses over the white line. See the web-published Volgovian Nutcracker for an example. I think the Roadblock rules from The Coast also use stage changes as a trigger -- it causes the roadblock to go away.
What is the significance of being in the red numbers?
Like you said, it's just a couple of cards. The Reluctant Hero secret is the only one I can think of off hand.