I think the problem here is neither the nut nor the deflation technique. The issue here was the location of the bead in relationship to the rubber tube around the valve stem. When a presta tube inside deflates, it doesn't retract the valve significantly. Having it nutted there is fine. After all, the rubber stretches.

But if you don't have the bead seated and the tube is pinched between bead and the hard thick base of the valve stem, then when you inflate the tube, the bead may do a number of things like slice through the tube, which may hold pressure because the cut is not exposed and pressure by the bead on the cut keeps it closed until deflation. Or the bead could blow off and the tire explodes partly off the rim in a lot bang and you blow the tube as well.

The way you avoid the problem is to mount the outer tire first PRIOR to securing the valve stem nut. I seat the tire completely, then push the valve into the tire and especially check the seat on the bead around the valve area, as the tube is a bit thicker and stiffer there and makes it harder for the tire to seat properly onto the rim at that point. Pushing up on the valve stem gently lets the bead drop into the sides of the clincher rim. As for the nut, some folks ride fine with it. I like the nut because it holds the valve firm and keeps it centered on the hole with less wobble while pumping and riding, so less chance of abrasion forming small cuts over time on the joint where rubber meets up with the base of valve stem.