According to Michael Daugherty's bio, he is "one of the most frequently commissioned, programmed, and recorded composers on the American concert music scene today." He studied at North Texas, The Manhattan School of Music, IRCAM and Yale (not too shabby), and currently teaches composition at Michigan (also not befitting the shabbiness department). Here he is on YouTube doing something many in his profession would like to see outlawed:
Many thoughts come to mind. Here is a renowned composer based at a renowned school who not only thinks it's permissible to work this way, but apparently does so himself, at least some of the time. He apparently is also confident enough in the results to out himself on YouTube, where pointy-headed colleagues at other schools (if they've yet learned of and figured out how to use the internet) might catch him. This is progress.
Whether or not it was intended this way, I also see this video as an advertisement for his (and, implicitly, the department's) openness to students who compose acoustic concert music using computers and software. This has to be something many prospective students wonder about when applying to a school, and it's not like you can just ask, especially if you fear the worst. Good for them for going right out and answering that question, and a further pat on the back for what is undoubtedly a shrewd business decision.
Having said all of that, I wonder if what we see here isn't also a busy composer attempting to balance a full-time academic job with a successful freelance career, and whadya know, he gets tabbed to make a silly promotional video for the university, which expects him to offer an accessible explanation of the modern concert composer's craft in less than four minutes. Who knows? Maybe this was the easiest solution to that rather ridiculous demand and he whipped out his noligraph and parchment as soon as the cameras stopped rolling. I'm not betting on it, but it's possible. You do get the impression that convenience played a role, but given the can of worms this could open with the traditionalists, I doubt anyone would venture into this territory without a slightly better reason.
In any case, the key, as he says, is that anything a composer uses to capture their ideas is a technology. All technologies have their limitations, and all composers must overcome the limitations of their tools in order to be successful. Proving notation software to be unsuitable for composition involves more than merely showing that it has limitations; rather, one must demonstrate that these limitations are insurmountable.