It's my goal that EVERY physical recipe, vanilla or mod, produces +1 Scrap. (Someday, fluids recipes will produce similar Sludge)
Technically, that shouldn't be too hard: Just loop over data.raw.recipe in data-updates.lua or data-final-fixes.lua and add your scrap to their results. However, there's a catch.
While I like the idea that you can't produce things without consequences, I would limit that to recipes that actually have recipe.result or recipe.results. In Bio Industries, for example, we have recipes that produce absolutely nothing -- but while the machines crafting them are running, they create negative pollution (i.e., they absorb it). Letting such recipes create scrap would be entirely contrary to the purpose of these recipes: to reduce pollution.
I also wonder if the production of seeds, seedlings, and trees, of biomass, or of burning wood/woodpulp to charcoal (and coal etc. after more advanced research) should produce scrap. The ingredients are naturally grown; adding scrap makes sense for things that have ingredients made from processing ores (metal plates, steel, copper, modded ores etc.).
Perhaps you could add a way for other mods to blacklist their recipes with yours? All you can do is making wild guesses, at best, simply because it is impossible to know about every recipe created or modified by other mods. The authors of those mods will know, however, whether adding scrap to their recipes' output is reasonable.