SItuation: AN Intruder HMG is inside a smoke template outside cover and not in camo state. He has LoF to an enemy model (due to MSV2), activates and moves to partial cover (still inside the smoke template). As his second short skill he shoots at the enemy model, who shoots back at -6. Does the Intruder have partial cover? or is it like for camo that the opponent may choose to shoot at you at any point in you movement trajectory, for example before reaching cover? Does SSL2 change this (apart from ignoring the -6 mod)?
This. No SSL2 doesn't affect it. The Intruder counts as attacking for the entire order and so can be shot at anytime in their movement.
There is nothing in the Zero Visibility Zone rules saying that the default rules for moving targets are over-ridden.