2 months later, I decided to add a safety toggle for this. Either Factorio changed to allow this, or maybe I didn't test enough in the first place, but with the safety toggle off, items which exceed the stack limits of their ingredients will recycle to the stack limit. I distinctly remember items like that simply getting stuck in the machines, but maybe it was caused by something else.
EX: Nuclear reactor requiring 1000 concrete will produce 200 concrete (the default stack size) when recycled. It is a massive loss of ingredients, which is why the safety is on by default, but the loss can be minimized when combined with mods that change stack limits (or ignored if you simply send random crap items to be recycled).