It's the mining and research outposts (like Arcorp 141, shubin mining, rayari, etc.) that have the masks in the red boxes - There aren't any in the bunkers and I don't think they appear in the sites such as Bountiful Harvest or Bud's Growery (They seem to share the same loot tables as bunkers). I hadn't thought they occurred in the abandoned outposts, but I did find one of the large white crates at one which had contents that were similar to those in the red crates at the mining\research outposts and I believe someone has mentioned finding one there - Even if they do appear at the abandoned outposts, the loot boxes that would contain the masks are (in my experience) less common than the red ones at mining\research outposts.
You don't even need to worry about having a backpack - Loot from the box to "local inventory", and from there you can either transfer from local inventory to the ship when you get back in, or leave it there in the local inventory for the location (a character reset will also move it back to wherever you select as your new "home" as well).