I don't think the above is in the spirit of systemd. Ideally atd would parse /etc/sysconfig/atd itself¹ and set it's defaults accordingly.
I think this remark shows very cleanly why so many *feel* that there is something wrong with the systemd concept. May be it has some merits over sysinit, but:
It contradicts KISS. "atd" (or any other daemon) should do what it is designed for. If any init system wants to start it, it has to deal with "at", *not* the other way round. To me what you call "ideally" sounds just like a wrong way.
Just an observation, 2c as usual, by no means a try to start another discussion about this topic.