NEC ampacities are calculated using safety factors. A safety factor is a very broad engineering concept. In this case it's a factor that divides the amperage at which the conductor insulation failed in lab tests. The idea is to build in extra insurance against, manufacturing variances and defects, the varying quality of field installation, varying environmental conditions. You don't want real-world installations operating anywhere close to where conductors failed in the lab.
The derations required for temperature, multiple conductors, etc., are, in essence, additional safety factors.
Put it another way: yes, the NEC is 'overkill', but for very good reasons. It takes some really complicated data analysis and boils it down to some relatively simple rules so that you, the electrician, can install conductors without being 'borderline' dangerous. If a conductor burns up, then you really effed up; probably you made multiple mistakes. And if you follow the rules then almost never should 'bad luck' cause a fire.
Upsizing conductors to account for voltage drop so that equipment will operate properly or more efficiently is really a whole other question than whether NEC ratings are 'overkill'.