FYI the guide they're quoting is not for the usual installation but for hosting a seed box. Presumably the kind of thing you would spin up on a VPS and not use for anything else.
Yeah, I wonder how much of the long-standing Unix philosophy & consistency is lost by breaking with best practices. autotools seems to be written off by many younger (and non- C) developers and maintainers, but still, it would be good to stick to consistent conventions on that platform.