No, you see the "best" use of the system is situational at best and subjective. In long battles (5 mins or more) none of what you mentioned applies. The "best" use of the system is what I described, there no debating about it. The method has been tested and used by thousands of players it is the most efficient way to play during NMs.
You see that is not how a universal cool down timer works. I'm going to take a page from World of Warcraft's battle system. Not every skill triggers the UCD, only certain skills do and when they do the timer for the UCD isn't always the same. The UCD can also activate on skills that do not directly affect your target (ie buffs, heals, etc.) your positioning has nothing to do with how a UCD even works. Waiting for the stamina bar to regen produces the same combat effect as waiting for a UCD timer to run down. In both situations you can't perform any other actions, other than those not requiring stamina or those unaffected by a UCD.
Outside of a party situation where you're engaging mobs of appropriate rank the combat system varies greatly from when you're with a fully organized party. The differences are too great to even make a comparison thats what you don't understand. Even as a pugilist tanking NMs you will see stamina issues. Haymaker II, Jarring Strike II, are near useless on a NM they're just TP sinks because you will mostly likely miss and they do piss poor dmg and can't stack into BRs. Even our R50 weapon skill Simian Thrash is worthless in a NM hunting group. As a pugilist your man threat generation comes from how fast and often you hit (this is still in testing but we've narrowed it down to either how often you hit or how many criticals you land or both).
Yes you're right in a solo situation most people won't see an issue with the stamina bar at all in fact it works out very smoothly and it won't hamper your actions. During long battles only the opposite is true. That is all I've felt like I've typed the same stuff for three posts if you can't understand the reasoning here then you just need to go find out yourself.