Yes he always empty the extractor machine
Finally someone else having this bug! 
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These drops and crafts are not comparable like that. So, with numbers.
The first numbers i posted included an error because in flipping betwen pages I accidentally calculated the wear value of tallow vs. the time factor of hide. Corrected here:
It takes 12.5 hours to complete a full queue of fat, and it leaves you with 1500 essence (visually 2 stacks)
It takes 25 hours to complete a full queue of skin, and it leaves you with 3000 essence (visually 4 stacks)
Again, you’re doing this faster with coils, but the ratio remains the same.
Unless you sorted them well and each crafted the exact same number of batches of the exact same ingredients using the same skill, upgrades, guild buffs, etc… then worst case scenario is one person taking twice as long to finish their queue.
With all of that said, there have been some machine bugs in the game. There is a (small with no changes in years) but real chance you somehow triggered a bug.
For now try to match your conditions exactly for a couple of rounds and see if you don’t get the expected result. There are too many variables here that easily explain the scenario.
Craft epics are beacon related? I thought it was character with craft.
Not that it makes a difference for me as I basically utilize a crafter (except for recipes all skill pages basically the same) and a shop/portal keeper (has just one skill page.
Sorry back to topic 
Guild buffs are beacon related. You must currently have the guild running the buff as your main, and the workshop/machine have to be guild aligned.
Your crafting epics should work wherever you are.
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Ahhh didn’t read right them my bad