As a general rule, I only change the rules when I have a darn good reason for it. Others (including training agencies) may disagree with those reasons, but I've given all of my changes a lot of thought and can defend my decisions. Your examples were good issues and here's my thinking:
Diving without a dive flag...
I avoid diving with a flag whenever I can. Having seen too many of them used as targets by sailboats and jetskis, I think they generate too much traffic. I also think that they represent an entanglement and task loading hazard that can't be justified by their purported benefit. That said, in shallow water where there is a risk of vehicular traffic that can possibly hit me, I will shoot a marker even if I don't have a flag with me.
Diving solo...
I've been known to solo dive and will again, within very narrow limits: only at sites that I am VERY familiar with, in excellent environmental conditions, and never deep enough that I can't get to the surface on one breath of air. I also dive with full doubles and I turn after using one third of my gas. I've been diving for a long time and have had the opportunity and time to develop my skills and my confidence in the water to a high degree. I've also been unfortunate enough to find myself in some true emergency situations, but that's given me an understanding of how I may react to future emergencies, should one occur.
Diving without an alternate air source...
I always have an alternate air source - at the very least a back-up regulator. My normal dives are done with 120cf tanks rigged with H-valves or with doubles. I sometimes dive with stage or deco bottles, but only rarely with a pony.
Diving beyond the limits...
As far as I know, all of the agencies say something to the effect of "don't dive beyond recreational limits UNTIL YOU GET THE PROPER TRAINING." I got the training and I practice it. When it comes to technical diving, I'm considerably stickier about following rules.
Finally, I have to admit that on a dive to 20 or 25 feet I may skip the safety stop if I haven't been down for very long - basically the whole dive counts as a safety stop.
Which gets us back to why would you omit the safety stop? As far as I know, the agencies all still recommend it and the science that's being done in the field increasingly shows that they're a great idea that help to forestall a wide range of sub-clinical DCS-related problems.
Steven