The hiring market is a market, though.
You're bidding on talent.
If you have an infinite budget you can just outbid everyone, everywhere and get whoever you want. Companies like like Netflix do something like this.
If you don't have an infinite budget, you have to start making compromises. You can try to pay everyone according to the highest possible local salary you might compete against, but now you're arbitrarily paying more than you need to everywhere else. Could be fine if you have unlimited budget, but most companies don't.
So you could try to set a median pay that's higher than the LCOL targets but lower than Bay Area salaries. Now you're attractive to some talent, but other people won't consider your company because it pays less than their alternatives.
Location-agnostic pay is one of those things that sounds great when your company has limitless money (or feels like they do, as in ZIRP), but most companies at scale realize that they're either missing out on certain talent pools or spending unnecessarily to acquire people.
In the case of GitLab, the author was making a great compensation for their location. If the author had zero knowledge that other employees were getting paid more, would they have even cared about their own compensation?