Well for starters pfsense dns servers dnsmasq or unbound are not really meant as authoritative servers, and do not do zone transfers.. Not really something I would use in a production/enterprise dns setup to be honest. But if you want you really should have different fqdn for each site.. So for host in site A, host.sitea.domain.tld and in site B it would be host.siteb.domain.tld They could be same parent domain that way, or could just be host.siteadomain.tld and sitebdomain.tld etc..
You would then create domain overrides pointing to pfsense at the other site for the domain in question.
In scenario 2, to be honest you really should have a DC at that branch site.. If your not going to use a DC at that site, I would have your clients use both dhcp and dns from the main site DC, and would not use dhcp or dns on pfsense at all in this remote site.