systemd-resolved normally does use a separate protocol, specifically an NSS plugin (see /etc/nsswitch.conf). The DNS server part is mostly only there as a fallback/compatibility hack for software that tries to implement its own name resolution by reading /etc/hosts and /etc/resolv.conf and doing DNS queries.
I suppose "the DNS compatibility hack should follow DNS RFCs" is a reasonable argument... but applications normally go via the NSS plugin anyway, not via that fallback, so it probably wouldn't have helped you much.