I am not sure if something has changed in the code or if I just got extremely lucky/unlucky, but today when I randomized all of my ships at least 2/3 of the ships had the same hull image for 2 of their types, which never happened to me before.
For example, the Lanius ship had the exact same hull image for its A & B layout and the Zoltan ship had the same hull image for its A & C layout. You don't really need anything in place to prevent two ship types for choosing the same crew or weapon configuration because that is unlikely, but since the layout and hull image pools are a bit smaller maybe there does need to be something in place to make sure two types aren't the same.
EDIT: I also just realized that with v1.1.3 the file location is not getting saved. It will still say the right location when you open up the UI, but if you go back later and rebuild the flagship again the mod will be generated in the default location.
Also, today I was had the privilege of also playing a Lanius ship without oxygen, though I wasn't able to get mind control and pull off the reverse boarding/abduction strategy. However I did come across the event where a civilian ship is out of oxygen and you can dock and flood their ship with oxygen to help them out.
Somehow I was still able to help the, without an actual oxygen system.
Anyway, I think for ACE the Lanius should probably have a high possibility of getting the Requisition License augment, I found it hard not to kill everyone mercilessly for their scrap as a Lanius ship with no oxygen.