Big Sur Updates Reset Apache Files
Apache is not the only service whose configuration files get overwritten with every update. My annoyance is the SNMP daemon.
For Apache, I suggest that you stop using the Apple distributed Apache. Replace it with the Homebrew version.
The Homebrew version uses /usr/local/etc/httpd/ for configuration, /usr/local/var/www for document root and is completely independent of Apple's version and so will not get modified by macOS updates.
Just in case you are not familiar with Homebrew.  You will find numerous web postings about how to install and configure Apache under Homebrew - an example. And you are already aware that there have been other Apache questions in Ask Different.