are the loot drops set already as soon as you start the missing or can you switch out your gear for nomad gear right before you pickup the missing and boss rewards
usually the loot table rolls when u kill the npc not when u start a mission, scavenger doesn't guarantee a different item but a better version of the item the loot table roll.
Even if you are running the nomad set you will still have 0% Scavenging because it's bugged so there is no point on using 100% use 80-99 to get better rolls.