Wow... ok figured it out. The links provided in @Gertjan post put me on the right path. It seemed strange that only Ubuntu Server hosts were affected so I started digging on that. Turns out that by default in Ubuntu Server systemd-resolved is not configured to use the domains passed by DHCP (either v4 or v6) not by RDNSS. So all I had to do was to edit /etc/systemd/networks/networkd.conf to have UseDomain=true and just like that, by magic the hostname is properly registered in Unbound...