Based on the comment by Felipe Sabino above I worked out the following. The permissions file of iOS for Xcode 6 is stored at location: ~/Library/Developer/CoreSimulator/Devices/<device>/data/Library/TCC/TCC.db. So we modify the db file using sqlite3 on the console.
Used the following Perl script from terminal. This could be done in any language really. 
$folderLocations = `xcrun simctl list`; // running "xcrun simctl list" on terminal returns iOS device locations 
$currentUserID = `id -un`;              // get current user
chomp($currentUserID);                  // remove extra white space from user string
print "currentUserID: $currentUserID";  // debug logs
while($folderLocations =~ /iPad Air \((.{8}-.*?)\)/g) { // Use regex to loop through each iPad Air device found in $folderLocations. Insert the permissions in the database of each. 
    print "folderLocations <1>: $1\n";  // debug logs
    `sqlite3 /Users/$currentUserID/Library/Developer/CoreSimulator/Devices/$1/data/Library/TCC/TCC.db "insert into access values('kTCCServiceAddressBook','com.apple.store.MyApp', 0, 1, 0, 0)"`;
    print "\n";  // neat logs
}
This one overrides kTCCServiceAddressBook permission, but there is also kTCCServiceCalendar and kTCCServicePhotos.