Just wanted to update this thread and provide a conclusion.
As many of you had stated, the driver's side axle did in fact come unscrewed from the trans-axle. However this story does have a happy ending. My shop, Rennsport Porsche (the place I just had a clutch job completed), are providing the fix under warranty. They also stated that due to the bolts shearing/trans-axle unscrewing that part of the rear suspension became damaged, but they are fixing everything free of charge.
Even though I am slightly inconvenienced by not having the car for a couple days, they are also performing another alignment, and it has been a fairly painless process overall in dealing with them.
In the meantime though I'm driving my sport package equipped 2000 540i. All's well that ends well!
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