Who are you and what have you done with Stefan?
I don't understand the thought that you'd be more likely to lock up the front wheel from rapid application of the brake if you cover versus don't cover. A clumsy grab at the brakes is a clumsy grab at the brakes. My recollection is that the MSF wanted all four fingers used on the front brake, and that's difficult (though not impossible) while covering.

No, it's really me
I had the same thought as you about covering the front brake making one more prone to lockup of the front wheel, and I actually asked my MSF instructor.
Her explanation was that its true that a clumsy "grab" at the front brake while covering or not covering could lead to the lockup, but by actually having to reach for the front brake (because you weren't covering it) it was a more decision oriented action. That is, it was a conscious decision to apply the brakes (however you were going to apply them)
In my class, two people locked up the brakes and washed out (one got pretty banged up) on the excercise where you brake in a turn by straigtening the bike first, then applying the brakes.
Both of those people (one guy, one girl) were covering the brake before entering the corner. I was watching when the guy went down pretty closely, and it was obvious by the way he completely straightened his arms and locked them, that he panicked and wasn't thinking about braking, more than he was simply grabbing onto anything he could hang on to.
Had he not been covering the brake, he probably would have just stopped long, or locked up the rear only.
It's different in every situation of course, but in MSF it has to be partly due to playing the odds of which is safer, and also reducing complexity because it's easier to teach it as being one of the other (brakes, or throttle) instead of teaching the fine art of modulating the brakes while simultaneously working the throttle...
Stefan