Provided your rear end lift was done with the 3" coils then yes, you can add a 1" spacer on top of them if more lift is desired.
It should be the majority of the lift kit. Crossmember drop brackets, diff drop brackets, steering knuckles, strut spacers, rear springs, rear track bar drop bracket... this is assuming a true 4" lift VS a true 6" lift. I'm not sure what, if any, parts that Zone crosses over between their kits. I could talk to my rep at Zone and look into this for you if you'd like.
No. Although it does seem like that should be the case, that's not how it works. Most 6" kits actually provide 5.5" of lift out of the box. So already we lost a 1/2". On a Zone kit (and others) 5/8" of that lift is from a preload spacer that's installed on the OEM strut. When you use Bilsteins you don't install the preload spacers as the Bilsteins provide the preload for you. So now we're down to 4 7/8" from the strut spacer plus whatever the Bilsteins are set at. So in the case of 2.1" you end up with a total front end lift height of ~ 7.0"