Tried to grab some pictures but they came out relatively useless. In any case, looking at the pictures and the video and the thread you linked... all of my mounts were in the proper position. Not unexpected as they haven't been messed with.
Pulled the insert out, replaced bolt with the new one I picked up in sad anticipation of this day. I had planned to drive around with the skid plate uninstalled, and maybe even unibrace ubq uninstalled (with the insert still in) but laziness got the best of me. Getting the car up on four stands is a PITA, didn't want to do it twice.
Car is back to being civilized, no vibrations to be felt at all. Drove around with the A/C on, happy to make extended pauses at stop signs just to enjoy it. I can also now roll the windows down without feeling the vibration resonate through the cabin. I thought I might notice the car being slightly less responsive with it uninstalled but I couldn't tell a difference. I've been spoiled in that area by driving my wife's Tesla. It has all the torques at all the wheels all the time, haha.
With the way my vibration resonated through the entire vehicle... is it possible that what was a practically imperceptible increase in vibration (in your experience) was amplified by my having the heavy duty skid plate and the unibrace UBQ installed?
I didn't bother with a new bolt, just loctite'd the old one. That bolt is seriously oversized for what it's supposed to do, the only way to break it would be maybe launching head-on into a wall at 100mph so the engine ends up in the trunk
I replaced the bolt on the GTI when I put the BFI insert in, but then I reused it when I replaced the mounts (the 2 pucks); many hard laps on track later, everything is tight to this day.
It's possible the for the skidplate to maybe amplify vibrations, but I really don't feel any in either of my Golfs and you said you can't feel any without the insert.. That's why I suggested engine misalignment, since I can't think of anything else.