Doc, your configuration is full of suprises you are revealing to us only piece by piece: 
A separate dnsmasq instance, libvirt, a VPN of undisclosed provenience, SELinux, and now NetworkManager and a probably not yet supported Fedora release... 
Any more surprises, and I am going to call it a premature xmas 
@devs: Any chances to have the template ask for some of the basics that would reduce our guesswork, for future topics?
NetworkManager is another tool that starts its own dnsmasq by default.
Your netstat -nltup shows a dnsmasq intance running alongside pihole-FTL, which may still lead to conflicts. I think the link I provided above contains some details on how to disable that for NM (towards the end).
I agree that this is likely not the cause for Could not activate remote peer, but I suspect resolv.conf to be involved in this as well.
A multitude of network daemons may be using that file, including but not limited to systemd-resolvd, NetworkManager and dhclient, as may Pi-hole v4 during installation (but that should be confirmed by a dev).
Have you probed into my hint at verifying that systemd-resolved is up and running yet?