I definitively go longer than the bottle instructions say, that's a fact, and dilute it a bit more than most folks. My reasoning is letting the plants actually absorb it and hope that their vascular system sucks a bit up INTO the lower stem.
When in doubt, yup stick with the instructions on the bottle. And don't be afraid to tweak concentration and contact time to dial it in for your situation.
Edit: i would keep an eye on that paper towel and remove it as soon as it seems saturated just to prevent things getting stagnant down there, I truly fear fungus in cloners