I doesn't count towards armor. It counts as damage resistance. Armor % is the first thing taken into consideration when you get shot, then damage resistance. So if you have maxed armor and 20% elite protection and then get shot by an elite for 100k first it'll look at the armor and reduce that down to 45k and then it looks at your elite protection and will take that 45k down another 20%. Not sure what the resistance cap is but I've seen a video of someone getting 97% with maxed electronics and mobile cover and Smart Cover combined.