Not necessarily "in the know", but...
1: Mandatories - do pirates pull mandatories in "ally" empire space? If so, last I checked there only needs to be 1 hex per empire on the map, so these empires can get 1 hex in each corner, and they can be declared off limits, the rest of the empire map can be neutral... otherwise, ally all the cartels to all the empires...
2: Engine Doubling: last I knew, there is an sfc.ini setting that shuts engine doubling off, but that's not a file that can be crc-checked