And another update in my "blog".
In Pihole you can set "Use Conditional forwarding" and list your domain and pfsense ip.
That way I can resolve my own internal domain and at the same time use 1.0.0.3 and 1.1.1.3 for dns lookup without going to pfsense. No need to copy over the hosts file.
I ended up not launch resolver and forwarder in parallel.
My setup now is that I Port forward all dns request on all interfaces except the kids-vlan to my pihole-1, I then portforward request coming on my kids vlan to 53 to pihole-2. I allow outgoing requests from my pihole-1 and pihole-2.
Regards. D