You need to set the following in your homeserver.yaml :
serve_server_wellknown: true
read more here: https://matrix-org.github.io/synapse/latest/usage/configuration/config_documentation.html#serve_server_wellknown
Also remember to restart your container.
I’m not sure if that is the best/correct way to do it.
What you should have probably done is use the
server_nameproperty to point to your Apex/Main domain.https://matrix-org.github.io/synapse/latest/usage/configuration/config_documentation.html#server_name
I highly recommend that you to go through the documentation throughly atleast once, especially if you will be hosting the server for a long period of time.
Edit:
If you followed the cloudfare guide you linked below, it should probably be fine. Still do go through the documentation.