In general I am inclined to agree with you. Given two equivalent libraries, if one is standard and one is pulled from github, the standard library should be preferred. If it were just a matter of developer ergonomics, I would agree with you in this case too.

But the command line interface is the fundamental user-facing piece of a command-line program. If it's not intuitive and clean, the usability of the whole program suffers. The internal API is secondary (this is why I didn't try to "improve" anything here -- go's flag package is good enough and I'm not trying to reinvent the wheel). It's all about a good experience for users, and I don't think Go's stdlib flag package provides that.

Commandline programs written in Go shouldn't feel like idiomatic Go programs, they should feel like idiomatic commandline programs.