This actually needs to be a BUG REPORT.
The agvtool tool fails when the key GENERATE_INFOPLIST_FILE is present.
I assume that the agvtool tool is looking for the key INFOPLIST_FILE, but isn't coded correctly to exclude a result of INFOPLIST_FILE being prefixed with GENERATE_, so it tries to find the location of the Info.plist file using GENERATE_INFOPLIST_FILE value of YES. Which FAILS.
If a dev wants to add custom fields to Info.plist, then an Info.plist is still written to disk at the location specified by INFOPLIST_FILE.
Cheers.