I just cannot figure out why I have take cover and crouch are two different options. I don't see any practical difference, can someone explain what the difference is, if any. I know you will roll into a cover spot but what other difference is there.

Is is common now to use a stim to boost your accuracy instead of augments?

the roll into cover is useful because it gives you immunity to ranged attacks in an arc ~90 degrees in front of you. this only works if you stay behind cover and only against ranged attacks, not tech or force. technically, you don't have to use the roll, if you walk up to a low object and crouch down behind it, it usually gives the same benefit, but rolling into position is faster and guarantees correct placement for the immunity. as far as shooting back, i am not sure how exactly it works. i think it works off of the visual animation. so for example, if i pop up with an instant snipe, i am only exposed for about half of the 1.5 sec global and still gain ranged immunity during the second half (down half) of that global, but i am not 100% sure on that. with typical warzone lag, it is hard to tell exactly.

using accuracy stims is an excellent idea if you are mainly a pvper that sometimes does hm ops. it allows you to replace the accuracy that you don't need for pvp and just use a stim if you go do an op. note that story mode bosses do not have the defense buff that hm and nim do so you don't need any accuracy for them. again, only hm and nim.