Fleet-before-Rancher Conflicts with Rancher-with-Fleet?

On our clusters we pre-install Fleet using the rke2/manifests directory. We then point Fleet at a Git repo that installs other items including Rancher. Rancher 2.6 bundles and requires Fleet.

My question is how do these two installations of Fleet play with each other? The cluster isn’t working well, some items were installed and then uninstalled by Fleet. Is it a bad idea to install Rancher 2.6 using Fleet?