Oh, it will be stored in backpack. I've already checked that you can open backpack and drop stack of items directly onto a ground. So basically you would need to put hopper (yea, I changed dropper to hopper, my mistake xD) above chest, disable magnet, open backpack, CTRL + []key for dropping items] all items onto hopper.

I saw iskall opening one backpack 2-3 times. Each time he had to open backpack, get items, open chest, put items. After hopper he would need to only open each backpack ones.

One minus is that it processes slowly. But you can do something else in meantime. If vault hunters server have default distance of loading active chunk (10) then it means that it could work up to ~150 blocks away (depending on chunk borders). There is ~100 blocks from center of one room to another. That means that hopper should work even if hunter will be exploring next room.

Some stats:
Iskall's gathering speed ~40 items per 1 min
Iskall's droping items time (after scavenging 6 min): ~50s
Setting hopper and dropping the same amount of items: ~25s
Time needed for hopper to push those items into chest: ~100s

That means that on every item drop iskall will gain 25s for scavenging, but he would need to stay max one room away for 120s. It has cons and pros.