You should be able to set it up, which seems to be the crux of your question.
The reason for the conflict is likely that the traffic is encrypted through the tunnel, but cloudflare holds the certificates needed to verify the identity of your site and can see all the traffic.
But tunnels are done by having your server initiate the connection with cloudflare, so it behaves like a client in terms of networking, and it should work in most cases.
(Worth noting that video was against their policies for using at least the free tunnels last I was aware, so if that’s part of your use case you might not be able to use it.)