Salem

Had a planters pouch in backpack which was not open and threshed some cereal seeds. They still went into that pouch and diluted the purity of the seeds. Is this normal?

yes.

I thought items in a closed backpack were immune to change from crafting?

If I put sea island cotton in the backpack and close it that does not get used to craft cloth. Why are seeds different?

That's not crafting though. That's auto-adding to inventory, which always goes into whatever container there is first. That's why the silver always goes into your purse until it's full.

Not trying to be difficult but threshing seeds is in the crafting window under miscellaneous.

Yes, but seeds are a product of the recipe, not an ingredient.