If that's what they did, and I wouldn't have thought the shaft would flex far enough to enable the box to drop out, then they would have left the shaft hanging by the pinion joint, or had to wire it up out of the way. Either way, this can't have been good for the universals or the CV joint and I'd still like them to explain how they did the job, and to examine the shaft properly.
And, after all was sorted out, I would still use another mechanic next time. If they did things this way, they are butchers, not proper mechanics.