Having test played Brutal-AI with Piratez myself, I can tell you about my firsthand experiences. Long story short, while running it is possible, there's some complications that make this inadvisable to outright.
First, it will radically change the way AI behaves - by default, Brutal AI shares information between enemies as well as the player going on better. This means there are few to no campers, every single enemy will start rushing towards your position. So most fights boil down to can you hold your position or be overrun, with very little maneuver on your part. Giving how assault-focused Piratez can, and arguably should, be, it's not an improvement for the better in terms of gameplay experience.
And yes, whatever code used for enemies to ignore neutral units in certain missions, i.e. damsels, doesn't work in the BrutalAI version.
Regarding X-Com Files, I enjoyed playing it because is yes, you will at one point be expected to fight scores of humanoid enemies with just a handful of agents. However, with good tactics and superior training and equipment, it is possible for a small elite force to prevail even when greatly outnumbered. High quality weapons to make sure your volleys are deadly, grenades for crowd control, body armor to increase agent survivability, and a few others tricks. Enjoy it while it lasts and the tables turn when you need to deal with alien expeditions using a mass army ill-equipped for their weapons.