Yes, but this is a mere terminology problem. Beeminder is the very embodiment systems over goals.
On the one hand, I agree. In fact, using Beeminder for goals (per Adams) is so rare that we don’t even have a good term for it. “Short term Beeminding” is the closest thing I’ve heard. And even then you are usually turning it into a system accomplish the goal in a granular way. Using Beeminder to track a boolean Done/Not_Done is not very useful.
However, I have to point out there are parts of the Beeminder UI which live in the goals world. When I use Beeminder as a system I just ignore them:
I think Adams would have less of a point if the road dial supported [∞, None, $RATE] and UI elements corresponding to the goal being accomplished were hidden or otherwise took advantage of the knowledge that this goal is actually a system.