> use paper as a data processing medium

I also do the same thing.

> I don’t want all that mess in the capital-N Notebook, but it is hard to know when to switch from backs of envelopes to the Notebook.

On the contrary, I want and enjoy recording my failures, false starts in these notebooks. These are important lessons. A culmination of "what not to do"s, or "Lessons Learnt" in NASA parlance.

My engineering notebooks are my messy garages with working things on the workbench and not working things in a pile at the corner, recording how I think, what I think, and what works / what not.

The code is the distilled version of what's working, the "second" prototype, and the polished product.

Creation is messy, and there's no running away from that. Keeping the mess in its own place allows incubation of nice things and diving back into the same mess to find parts which works beautifully elsewhere.

I prefer to embrace the suck and document it too.