O servidor ISC DHCP possui zonas, o que poderia resolver seu problema, mas duvido que você deseje deixar o dnsmasq.
Mas você pode iniciar duas instâncias do dnsmasq com configurações ligeiramente diferentes. Interno:
bind-interfaces
interface=eth0 # internal
dhcp-range=192.168.1.2,192.168.1.254,12h
domain=mydomain.eu
no-hosts
addn-hosts=/etc/hosts.dyndns # hosts file created by my dynDNS server
expand-hosts
# Server/VMs
host-record=server,192.168.1.1
host-record=server.mydomain.eu,192.168.1.1
cname=dns.mydomain.eu,server.mydomain.eu
address=/mydomain.eu/<externalIP> # wildcard subdomains
e externo:
bind-interfaces
interface=eth1 # external
no-hosts
addn-hosts=/etc/hosts.dyndns # hosts file created by my dynDNS server
# Server/VMs
host-record=server.mydomain.eu,<externalIP>
cname=dns.mydomain.eu,server.mydomain.eu
address=/mydomain.eu/<externalIP> # wildcard subdomains