Here's the problem: Imagine a queue with 2 packages in it, the 1st package uses crossdirect and the second uses cross-native. When building the 1st package, pmb will configure the native chroot for crossdirect as expected. When it gets to the 2nd package, the chroot env/config might not be appropriate for actually doing a native cross compile.
This re-inits the cross compiler stuff if the cross compile method changes while processing the queue.
Another approach that might solve this problem is to not re-use chroots when building packages... I didn't think this was a good way to go because it would greatly increase runtime (having to recreate chroots multiple times)