There shouldn't be any penalty for using stale fat or a mix of fat and bark. I can't remember if spoiled fat works. If you use the fat from the animal you can reduce penalties to 0. If you use bark, 99.9% of the time if you'll get at least a 1% penalty since the unused will be in your inventory.
You seem to be implying that the weight penalty of the clean skin and of the tanning agent used in the tanning process is not counted when you apply tanning agent to a clean skin. Do you KNOW this to be true? I know that it shows no penalty at the END of the process, or DURING the process, as the hide is placed on the ground as soon as the process begins. But my understanding is that only the penalty at the beginning of a crafting process matters and it seems quite possible that the penalty is applied before the skin is dropped on the ground, depending on what order the steps of the crafting process are carried out by the game.
The same question applies to cooking. If I have 10 cuts and nothing else in my inventory and I roast them, is the penalty from the weight of the cuts applied against the cooking result?
These questions are rather autistic, but I'd rather learn to craft the optimal way and then not worry about it than continuously craft suboptimally. That's one of my tiny pet peeves is the seemingly random way in which items can either be nearby or must be in your inventory in order to craft something. If it were up to me, tools would always have to be in your inventory, as would any raw materials smaller than a slender trunk. Or just tools, and raw materials can always be nearby but not in your inventory. But, for instance, when you're drying meat, I believe the only thing that MUST be in your inventory is the tying equipment, which doesn't make a whole lot of sense.