Through various tests I'm also stuck.
I went into the trampoline project and fixed it so that Unity by default builds for iOSDevice instead of Simulator - to get rid of that "first time thing".
But I still get the missing ipa at path MISSING error. Seems like the script is trying to look at a wrong pathname and/or its not waiting until the compression process is completed. Noticed a few times by monitoring the build folder that the ipa file appears after the error message pops (2-3 seconds).
Then again we got a somewhat large project (250'ish mb uncompressed .app), so might be something with that. But when manually trying to "Locate ipa file", it doesnt allow me to pick the final .ipa file - so the filename its looking at might be wrong as well.
Manually trying to build the project in xcode fails as well (the project generated by Auto Pilot)! Building the project via normal Unity xcode build process works.
I've given up for now and hope that a Skype support session can fix it.