When using Cloudflare DNS entries for reverse-proxy hostnames those hostnames will resolve to the Cloudflare IP, but inside the home network they should resolve to the internal server IP.
When using Pi-hole as the internal DNS server you can customize the IP returned for domains/hostnames by doing the following.
First, create a custom configuration file to tell dnsmasq where to find additional hostname information for the LAN:
$ echo "addn-hosts=/etc/pihole/lan.list" | sudo tee /etc/dnsmasq.d/02-lan.conf
/etc/pihole/lan.list with lines with the format
ipaddress hostname [hostname]...
192.168.1.75 ombi.mydomain.com tautulli.mydomain.com mediaserver
Finally, restart the Pi-hole DNS server:
$ sudo pihole restartdns