A level 2 is indeed worth it, a level 3 absolutely not!
I usually get around 55 pies instead of 50 from the mixer. When cooking them in a furnace there is indeed another chance of getting a bonus but that seems kinda finicky, when I put 5 stacks of 50 in 5 different furnaces usually 3 or 4 come out as 50, the rest can have a few more and sometimes a lot more but the latter happens rarely.