genrally all hardware elements are designed to a certain power spec, yet they are based on the default settings for the component graphics card etc.
If your going to overclock then all them specs are useless. You cant overpower a system provided the PSU is as you say a quality/trusted unit. Yet if you go too small then the PSU wont last very long whatever the manufacturer or quality.
What is great about modern switch mode PSU is there efficiency. if you dont use the power it wont drain it, well apart from the idle power which will be genrally the same for a small psu or a more powerfull psu.
Eg. 95% efficency on 500w is more efficient that 95% on 1000w so the power lost in heat is of course more for 1000w. zippy do a very powerfull PSU and very high efficiency closer to 98%. all depends on what you want really lol.
you also need concider that as system gets older its power drain increases, when you upgrade your system 'add anouther hdd' it all changes etc. Good to always add 30% extra headroom to a design to allow for certain things.
Last but not least lets not forget about start up currents, the nasty power on drain.
As to answer your question huron: Experience in electronics is how we can make the assumption, its easy to generally work it out in ones head easy enough from knowing how and what hardware requires and how it drains power, how it works etc.
That calculator looks good, i would say add a bit more to the end of the calculation after you use it. The calculator does not have a entry for enviromental settings, silicon conducts and drains more power when hotter not to mention runs much faster at higher temps 40'c optimal. To hot = thermal runaway, too could makes silicon an insulator and wont conduct. HDDs use more power at higher temps aswell as noisy enviroments so loud fans, music, tumble dryers etc will cause a change again.