Actually, the difference is a little more fundamental between hall and VR. A VR is simply a coil of wire with a magnet and toothed wheel, the output is an asymmetric A/C signal that varies frequency and voltage with RPM (like a generator). The Hall is a transistor that is sensitive to magnetic fields and it turns on and off with the trigger wheel. It's output is more of a square wave that toggles from high to low. It never goes negative like the VR.
None of that means a hall sensor can't toggle the VR input, but it has to be adjusted to look for the right signal inflections.
I'm using the VR in a MDS dizzy. I had similar problems at first. In order for MS to see the tach signal at a slow enough RPM, I had to turn down the trigger point on the VR circuits to the point I was getting extra trigger events too. My solution was to close down the air gap (increases the output voltage) and turn up the trigger point so it was enough above the noise level to not give false triggers.
For your case, if the hall can take the full 12V (I would expect it could) that will raise the voltage of the high signal. Another problem I had was I installed one of my pots backwards, so when they say turn clockwise, I have to turn counter clockwise. hat wasted about 2 hours figuring out. Unfortunately, I'm guessing there's no easy way for you to run the trigger wheel without cranking the engine. I had it easy. I hooked the dizzy to my cordless drill and could run it from 0 to 3600 RPM (would be 7200 crank RPM) with the squeeze of a trigger.
So, if you up the supply voltage to the hall, run it's gap on the tight side, that will maximize your trigger signal. Doing that will allow you to adjust the VR conditioner to trigger at points high enough to filter the noise signals that are now triggering your MS. Check this.
Adjusting the V3 Main Board VR Input Circuit Potentiometers