systemd's behavior is completely reasonable. The folks arguing otherwise on the issue would probably be better served by installing dnsmasq locally to do what they want and pointing systemd at that.

It may be worth pointing out that dnsmasq has a similar behavior by default and points out the correct way to override specific hostnames/zones:

Q: My company's nameserver knows about some names which aren't in the public DNS. Even though I put it first in /etc/resolv.conf, it doesn't work: dnsmasq seems not to use the nameservers in the order given. What am I doing wrong?

A: By default, dnsmasq treats all the nameservers it knows about as equal: it picks the one to use using an algorithm designed to avoid nameservers which aren't responding. To make dnsmasq use the servers in order, give it the -o flag. If you want some queries sent to a special server, think about using the -S flag to give the IP address of that server, and telling dnsmasq exactly which domains to use the server for.