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. 

For the curse cards, I did consider some of these complications. I have a mini "law of root" document attached that goes over the complications with curse cards. 

My ruling was that curse cards cannot be placed into special zones like the Decree / the Retinue, since curse cards don't have a suit so they couldn't be used to do anything. (And in the Eyrie case they would immediately turmoil).  I didn't consider the case with the Eyrie where they MUST place a card and have only curses in hand. I think in this case it would make sense that they would have to use the discard mechanism to replace a curse with a real card, so that they would have something to put in the decree.