The bootstrap code makes assumptions about the future of the js spec and browser implementations that aren't safe. Young people don't remember the dark days of people writing js to leverage IE/Netscape specific bugs which then had to be turned into features because so much code existed in the wild that could be broken.
Crockford is a scarred veteran of the spec wars. I'm sure that when he sees young people trying to game spec/implementation ambiguities, he thinks, "Never again! Not on my watch!"
I think best practice is explicit, future-proofed code that doesn't tie the hands of spec authors or browser vendors. I know that Crockford's tool doesn't accept the current spec or browser behaviour, but his choice is informed by past experience and concern for the future. It's not just some random bug that he's too stupid or stubborn to fix.