Good question about the omens track. Yes, the points are only when revealed, like sympathy. I actually put a lot of thoughts into back-loading those points at the end. Here's my thought process:
Cursed players have a decision to make: Do they get rid of the curse with a Favor, or give the Augurs an Omen? Using an Omen means the Augurs improve their engine, but a Favor can be used against you specifically, so you know it's going to mess you up later. Putting in the points at the end of the track means that in the end game, it's a completely different calculation. Suddenly it's not "Whatever they get one more action", it's "Oh shoot this could put them in range to win next turn". So basically it's a way to heavily incentive paying with a Favor (or holding on to the curse). This also gives the Augurs more policing power / increases entanglement towards the end of the game, which I think is a fun dynamic.
Pyramid steps are sort of like strongholds. They don't cover anything on the board, they just chill in your supply until you build them. It's sort of like an action tax for getting a pyramid knocked over.
Pyramids and favors aren't connected at all, they just ended up in the same place on the faction board. I guess if I keep working on this I can give them their own box to make that more clear.