I have just started to learn the art of the BC, and I seem to have better control of the spool using the tip of my thumb just underneath the fingernail than using the meaty part of my actual thumb. Is this acceptable, or should I only use the "standard" technique and nip this in the bud?

I would say as long as you can control it this way its no problem.  Sometimes I will make a cast and switch hands while the bait is in the air and actually feather the spool with an index finger.  I didn't notice I was doing it until recently.