I have seen that many times, as well as seeing people use it about themselves.

Geek, nerd, and dork can all be used positively/affectionately. I know I've called myself and friends all of the above on many occasions.

As one of the unsupervised dorks working on LLMs at Meta (not one of the authors here) I took it in a positive way :)

I think Noah Kagan's blog is literally called "OK Dork", and I always assumed the title was self-deprecating (in a fun/positive way) rather than negative.