IoT not working with Pi-Hole

Yes if Pi-hole were doing DHCP services for your LAN.
Then you can tag a MAC address and have a customized DNS server (1.1.1.1) pushed to that MAC via the embedded dnsmasq DHCP option below (MAC 0C:2F:B0:XX:XX:XX as an example):

dhcp-host=0C:2F:B0:XX:XX:XX,set:cloudflare
dhcp-option=tag:cloudflare,option:dns-server,1.1.1.1,1.0.0.1

Settings > DHCP Settings > Expert > All settings > Miscellaneous > misc.dnsmasq_lines

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