@Hangnail6119 Ok few updates that I found out after digging a lot more.
In the S2S config pfsense uses transit network IP address so if you have a tunnel as in the video 10.100.90.0/31 that means your sites when sending requests to other end will use that tunnel ips: 10.100.90.0 and 10.100.90.1 Firewall that is asked for a DNS record needs to have Access Lists record for the tunnel. Otherwise it will just refuse those requests. You don't need to add other firewall as DNS server you just need to define Domain override.With that knowledge how would my example work:
I have 2 sites connected with a tunnel: 10.100.90.0/31
SITE_1 with IP: 10.100.90.0
SITE_2 with IP: 10.100.90.1
SITE_1 has some servers under domain example.com and SITE_2 wants to access them
SITE_1 has host overrides for single servises under Services > DNS Resolver > Host Overrides for example:
git.example.com points at some internal IP and SITE_2 will want to access that
SITE_1 will need to have Access List added for tunnel network Services > DNS Resolver > Access List > +Add and there tunnel network specified 10.100.90.0/31
SITE_! will also need a rule that allows it to recive DNS requests from other end of the tunnel, The simple rule ALLOW src:* dst:This Firewall(53) on S2S interface should be enough AFAIK(at least it works for me :P)
Now the only thing that SITE_2 needs to do is add Domain override. It's located under: Services > DNS Resolver > Domain Overrides and it needs 2 things example.com domain and IP address of SITE_1 that would be 10.100.90.0
And that was my problem, now everything works.