I organize my binders like the rulebook suggests. It would be nice to have all faction-related cards inside the binders, but green and black just have too many tokens. Instead I made a pile of hero cards, starter cards, worker cards and tokens (in this order) for each faction and put it separately into the box. This may consume more space when travelling with something other than the deluxe box, but it reduces startup time of the games as there is no need to fiddle the starting deck out of the binder.
For the neutral factions I built my own Finesse and Bashing binders. They have less cards so everything fits on one double page. Left: Spells and Tech I, Right: Tech II and Tech III
I am using the method of TheJTrain: If you remove the inlay all components fit nicely, even two or three additional playmats.