Here’s the pull request where they removed the script and the reasoning behind it: https://github.com/nextcloud/documentation/pull/431
I personally agree that it should still be mentioned in the installation guide somewhere making it more clear to people searching for it, however if you perform a new install using any method described on the manual, your permissions will end up being correct. That’s because they are already set in the archive you can download, and you only need to change ownership which is mentioned as part of the installation.
Ultimately the http user should have read write access to the core application files and data files, making updates super easy, in order to keep up on updates, in order to keep up on security fixes. It’s a trade off, instead of locking down files (which is less useful than it used to be) you make updates easier so less people get stuck with out of date versions of nextcloud with known vulnerabilities.
If you want, you can totally lock down your files a bit more as long as you’re comfortable (and remember) to relax the permissions when you want to update.