Took a little while, but I found the issue 
It’s not a bug but a feature! (and really is a feature…) The default behavior, for performance reasons, is to only trigger pointer events on one controller. You can enable pointer events on all:
AR screen pinch debugging | Babylon.js Playground (babylonjs.com)
Now you can get the pointer down events of more than one finger.
Now - you will notive that the pointer event doesn’t have screenX and screenY, as webxr doesn’t provide us with this information. As you want to measure the distance between the two fingers, you can use the ray’s origin in the pointer info and measure the distance between those two points on each frame