the problem for me is not xcode 8 i have tested the following:
xcode 7 and ue4.12 works, xcode 7 and ue4.13 Fails, xcode 8 and ue4.12 works, xcode 8 and ue4.13 Fails.
What works for me with xcode 8 and ue4.13 is to download the provision and double click it (this installs it with xcode) and then manually import and select the same provision file in to ue4.13
for me one does not work without the other. Here is a pic with the same provision shown twice top one installed with xcode, the second manually imported.
using this method packed a couple of projects many times without any problems.