Interesting topic. On the second part, I agree. Why does qualifying take so much longer (when you add the qualifying heats together) than the main, which is the most important? If running a 3 qualifier, 1 main system, I'd rather run 1 qualifier and 3 mains. It makes the runs count more. Otherwise, we're bashing the crap out of our cars for three runs for what, a few feet of advantage? (assuming you're in the same main...multiple mains would be different I guess)
Simple answer? It's easier.
Oh, to partially answer perhaps why we don't do the fastest lap thing. A lot of software I've seen only counts to the tenth of a second. I suppose it would require a simple software change though. The other answers are good too.