The issue with the "buy the bike with the components" is that most bikes do not come with everything you want (or need). For example, I am building a trek 7.3fx for trails and commuting, and I need 25in (64cm). Trek does not make a higher fx in 25inch, and the components on the 7.3fx are mostly crap. I have no choice but to buy the bike whole, strip off most of the components, build the now empty frame with what I want (like 180mm cranks, etc), and sell the rest.

You can not buy a higher fx with xt parts, they all have road components... plus the stems, posts, bars, etc are never right from the factory...

All three of my bikes are basically the original frame with all new parts... yes it costs more, but I have exactly what I need.