IME, valve stem breaking free from the tube is down to the tire sliding on the rim, dragging the tube with it until the valve stem separates from the tube.
Again, IME, usually caused by low tire pressure. MTBers are more prone to seeing this than road riders. Folding tires are more prone to this than steel bead.
A couple of times I've coated the bead area of a folder with liquisole to increase friction.
Never needed it myself, but I've heard people using tubular glue to secure one side of the tire to the rim in extreme cases.

Poor pumping technique is often presented as a cause too.
Seems possible, but I've never busted a valve stem through pumping, and I can't say I've ever thought about how to inflate "gently".
Maybe I got lucky in my "natural" technique?

IME, stem nut or not doesn't seem to have much/if any influence.
Whether allowed to take a lean first, or held rigidly upright, if the tire creeps, the stem will tear.

Short valve in deep rim, a stem nut will make inflating easier though.

Presta valve in Schrader drilled rim, or Presta in Presta-drilled rim doesn't appear to do much either. I've run Presta-in-Schrader for decades without any issues reliably traceable to valve/rim mismatch.
Only thing "special" I do is that I use self-adhesive rim tapes, and cut my own valve holes. Don't use adapters, don't thread a valve nut on first.
Until they broke and fell off, I did use adapters on the hubside face of the rim.
You'd be AMAZED how quickly water seeps into the rim if you have Presta-in-Schrader and ride through a deep puddle or two.