Yes. Sadly, i can not do anything. For some reason, starting conditions do not work for base defense.
For explanation, starting conditions like allowed items, allowed vehicles, etc. work by removing disallowed items from the craft and sending them back to the base.
In base defense, these items are available because the mission takes everything from the base, not only from the craft.
I have nowhere else to send the disabled items, and they have to be located somewhere...
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As a replacement for the 'allowedItems' you could use the 'ignoreInBaseDefense' flag.
I don't think there is any workaround for 'allowedVehicles', I can add something if it's bothering someone too much.