The fact that correct or incorrect bolts were used is, IMO, a moot point. Ford's shop repair manual specifies that the bolts should be discarded in favor of new bolts when they are removed. The reason is that they are TTY bolts and by re-using them, their strength could be compromised. Frankly, this is Ford being extremely cautious - because this is a rather critical area - as many areas are if the car is anywhere its top speed of 211 MPH! But, old bolts or new bolts, they were not properly tightened. There is a specific star-patterned torque sequence for these bolts and there's just no way they are going to loosen up if this sequence was performed - per the manual.
The original TSB for the half-shaft bolts was actually for leaking CV joints.
This isn't quite true. The CV joints have stamped steel caps on them and under normal conditions these caps do not loosen or leak. I suppose that the loose bolts caused one of the stamped caps to work itself loose and then the grease could escape. The aforementioned TSB was for leaking transaxle fluid that had a habit of leaking down the splines of the transaxle output shaft and into the coupler connected by these 6 outer bolts.
FYI - I recently priced the halfshafts for another customer and they are about $900 and change from Ford. Best to get the shop to admit and take responsibility for improperly torqued coupler bolts which caused the situation. If I can be of help, please don't hesitate to call me.