I feel this way too. I even kind of like the no bullshit design ("design") on PHP's site as well. It's fast and it's clear and it makes me reminisce about the times when I didn't need a top of the line computer just to surf the fucking web.
I do like github and find it to be well organized as well, although it's search leaves something to be desired and sometimes I find myself fumbling through the UI to find a specific git feature. Although I'd argue that the breadth of functionality they need to cover is beyond that of a language site like PHP's.
On a complete sidenote, I've always thought github's 404 page was neat, but what does it have to do with good UX?
And, that doesn't inherently make it well-organized, nor does it say anything about how discoverable content is, or how well the interaction is with the commenting system, or anything else really.
It is a science, I implore you to read up more on it if you really think your anecdote is an example of 'good' UX (and by extension, design).
I'm not sure what the sciences say, but in my opinion good user experience starts with knowing who your audience is. I still argue that ~95% of php.net's audience is there for documentation reference. If 95% of your audience needs to simply look up a language construct or function, how can one to two page requests be perceived as bad UX?
I can literally type in http://php.net/[FUNCTION_NAME_HERE] and get exactly what I want. The only thing I need to memorize is a domain name. And if I'm too lazy for that, it's undoubtedly the #1 hit on Google.
Take for instance, one of the 1st things many might use the site for: downloading PHP. There's a downloads page, and then there's a Windows download page, and they're both fundamentally different. It's as if you're going to a completely different site, which breaks any continuity there was to begin with. Am I even still on php.net?
Likewise, what's the utility of the tutorial[1]? It directs the user to Apache's website to download a server, even though one has been bundled with PHP for 6 months now. A server that's included by default for the sole reason of making local development easier, but they can't even keep their "newbie" tutorial up-to-date even after 6 months?
Please don't get me wrong, I'm not trying php.net is /bad/; rather, I think there's room for improvement.