He didn't, right. The story is a good example of how in depth some design decisions can get when desire for perfection kicks in - as programmers that focus on products, we have to realize that purity is always a stresser of we don't go with our gut. OP could have just played 3 notes on a midi keyboard instead of coding with all the conversion and Perl and whatnot. He got what he wanted and its might cool but doing the same process for every design decision is going to stress anyone out in due time
I'd rather spend the time getting things Right. I'm a software guy, and I'd much rather return to code that's well organized and thought out. It takes time a iteration to get to well-designed code.
When I get outside my area of expertise (which is solving problems with code), I still like to spend time making things feel like they were professionally made. Doing that lends me credibility, make my own products more appealing for purchase, and give me lots of personal satisfaction.
To this specific story, even if the guy kept all the different music theory note sequence combinations in his head, he's bound to forget which he played and which he didn't. Hell, wrote a couple nested loops and be done with it. Go back after the few minutes it takes for the audio to render and listen to every combination, knocking out the bad ones, re-listening to the others honing in on a good one ... Sounds like a good automated/iterative balance to me. I'd have even automated the file slicing and put a text interface on it: play a sound, ask for Y/N input, keep looping the remaining Y responses ...
He spent 2 hours and created a sound that causes entire rooms of people to pat their pockets; I'm pretty sure it would have actually taken longer to try out samples by hand (and evaluate each one as you go).
The thing is, he could have done the same thing in about 20 minutes with a MIDI sequencer. The sound doesn't cause people to pat their pockets; the reason this sound works well as a ringtone is because it's easily recognizable while being sufficiently bland and short not to be outright annoying.