Hi, Alexander. I finally had time to go back and remind myself what the exact rules were regarding the villains. So, rules as written, if the NPC has a villain tag, then yes, they follow the same damage/condition rules as PCs. I agree, this can make them pretty tough. However, the most commonly applied damage from weapons is Chassis damage, so it should be possible (not easy, but possible) for the PCs to send a villain into negative Chassis repeatedly until they hit system failure.
Thankfully (for the PCs), only two stock foes have the villain tag (Apostles and Boilermakers), and then the 3 main baddies in the included adventure. I wanted the main big bads to be tough to take down. That's the DM in me who gets frustrated when a party takes out the main villain too easily.
That being said, I agree it's probably too hard as written. If I do an update (and this is a game I've been meaning to get back to at some point), I would probably come up with some other solution for making the villains challenging without using the PC rules. In the interim, you could certainly house-rule this if you play and say villains must be knocked to zero on a stat X number of times before they're destroyed.
I hope this helps. Let me know if you have any questions or suggestions for improving the game.
Best,
TS