The fluctuating readings on the Rotax powerplant have been reported before, but mostly with our amps shunt of course. We do think that the fluctuations are real - ie, that the alternator has a bit of a noisy power output. The way our EMS measures current internally prevents us from filtering the amps reading better electronically. We'd guess that there are only a few people out there using the GRT hall effect sensors at all. In any case, we haven't had complaints on them.
One thing you can try is to create and install an analog filter with a couple of components. I'll note that this proposed solution is ONLY designed for the hall effect sensor and will not work with the shunt (it would actually make things worse). To do this, install a 1Kohm resistor between hall effect and the EMS, and a 100uF capacitor between EMS wire (after the resistor from the hall effect) to ground. In engineering terms, this should damp 99% of 60 Hz or greater noise.
If you decide to try this solution, please post your results to this thread.