macOS Server App no longer saves Websites settings
First you should enable debug mode in Server.app by running the following command:

defaults write com.apple.ServerFoundation DebugModeEnabled YES


and restarting Server.app. This should enable the debug menu. Then make sure the "Log Actions To Server Log" item is checked. Rerun your test, and then look at the log file in ~/Library/Logs/Server.log. The file shows the request/response communications between the Server.app and the backend admin tools. Look for commands to servermgr_web, most commands are in plist format, though the web commands may be in a JSON format.

Look for writeSettings commands specifically.