when you don't have a throttle you need to control, I don't see a lot of reason not to brake with all four.
Reason: Steering control. The more fingers you have still on the handlebar, the more control you have over the steering of that handlebar.

I can not imagine riding trails with multiple fingers hovering over my brakes while only my pinky, or 2 fingers are wrapped around the handlebar. On a long tricky decent I noticed a marked decrease in hand fatigue when I changed to 1 finger braking (from 2), allowing all of my other fingers to remain on the grips.

With a motorcycle, you are not (I guess) negatively impacted by stearing by simply pressing on the handlebars. In MTB, I find the need to finess them, pull them toward me, push them away from me, etc frequently. I can't do that if I don't have fingers on the grips.

To raise my front wheel, for example, I press hard on the pedal while pulling toward me with the bars and leaning back. Imagine taking a long stick between your hands and breaking it with your foot. I don't imagine I could do that with all my fingers hovering over the brake lever. In fact, that would likely result in a very abrupt and unplanned stop!

This might be one of those cases where motorcycle techniques don't carry over very well. I've never ridden a motorcycle though, so I could be wrong.

Also, with a MTB set up properly for 1 finger braking, even if the lever DID come all the way to the handlebar, it would not catch my other fingers becuase it would be too far to the inside.