I did look at the article and I think the answer to your question is in the 3rd paragraph:

"There’s no better way to figure out the interplay between volume and various settings than by going hands on with your setup"

In this article what the author is essentially saying is you need a starting point - so set everything in the mids. But its just a starting point - because you have to start somewhere. You could start with everything at 0 if you wanted, it wouldn't make any difference - because as he states, once you have a base line - or starting point - start tweaking.

Also, I would say the author is not considering a modelling amp, but is most likely using a conventional tube amp. You might still be able to make this work however. I don't know what you have for a modelling amp, but on my Vox VT15 I can bypass the modelling effects and just use it as a conventional amp. You will need to find this out for yourself if yours can do this.

I know if I am not experimenting and playing with all the knobs, including those on the guitar, I am not learning what tones are possible. I have always found that I learn best when I just jump in with both feet and start mucking about.