I FINALLY FIXED IT!
Turns out it was not the upper strut mounts.
The actual fix took another year to diagnose and correct. In that time I changed my thrust bushings to poly type thinking that might fix it. Nope. Kept digging and retightening everything Nothing made a difference.
Eventually stumbled upon a great thread on a 5 series forum which perfectly mirrored my issue. I noticed that they were encouraging others to install a Grade 8 lock washer under the top most nut on the strut. Theres was a 9/16", ours is a 1/2". Thread
here.
Basically, when Bilstein designed the B6 front struts for the X1, they must have designed them to be used with stock height springs. The reason I say this is because there is an unthreaded portion of rod at the top of the strut that does not allow the top nut to be tightened down enough when a shorter spring is used. You think you have torqued the top nut down properly, when in actuality, you are just bottoming it out on the portion where the strut threads end and the unthreaded portion of the rod starts. By installing this 1/2" grade 8 lock washer, you are filling in that extra gap between the top of the upper strut mount and the end of those threads. Heck. It might even be smart to use two washers instead of just one. There is still a TON of thread remaining above the nut when just one washer is used.
I can say that the addition of this 1/2" lock washer has completely fixed my issue. I'd recommend it to anyone who is experiencing a pop from the upper portion of their strut tower over small, quick bumps or when stopping or going. A quick diagnosis would be to have someone push down on the front of your car while you listen at the front. You'll hear the popping as the strut moves up and down.