How to deactivate MacOS server apache
This command deactivates web services
$ sudo serveradmin stop web
These commands should unload the launch daemons inside Server app. Following my experience Server Apache takes over as soon as you install server app. Stopping web services in some cases is not sufficient. By unloading the Apache daemon server app is unable to start its Apache.
$ sudo launchctl unload -w /Applications/Server.app/Contents/ServerRoot/System/Library/LaunchDaemons/com.apple.server.httpd.plist
$ sudo launchctl unload -w /Applications/Server.app/Contents/ServerRoot/System/Library/LaunchDaemons/com.apple.serviceproxy.plist
When configuring Server’s Apache the following configuration files are used. By uncommenting any listen section Server Apache will not be able to run.
$ nano /Library/Server/Web/Config/Proxy/apache_serviceproxy.conf
$ nano /Library/Server/Web/Config/apache2/services/ACSServer.conf
When Server Apache does not know which ports it has to listen to, it does not run.
Depending from your system some steps or all of them might be necessary to stop Server Apache from running and for your Apache installation to take over. All these steps will only affect your server web services.
With the next Server App web service will be gone.