I have played my first run with this mod from a fresh start to the point where I have the flying bots online in strength.
The recent change where you added a toggle button to turn the drones on/off fixed what was, by far, my biggest gripe and made this mod really pretty good.
My biggest remaining issue with this mod as it stands right now is that their build radius is just too dang big. You'll just be minding your own business, trying to design and build some sort of array when all of a sudden half your drones run off to repair a couple of slightly damaged turrets and some walls 3 screens away. Oh, and there's a train coming. Splat, Splat, Boom. I would suggest reducing their build radius by at least half. I would also suggest making it configurable in the mod settings so we can tune it to our own preferences.
The next biggest issue I see has to do with vehicles. I think it's fine and good that the bots don't deploy when you're in a vehicle but there is an issue with their behavior when they try to return to the player and the player is inside of their tank or car. They tend to get stuck on the front or back of the vehicle. Additionally, if your vehicle is moving, when you attempt to stop to let the bot board, the bot tends to run into the back of the tank before the tank has fully stopped and get themselves run over. If it's possible, I would suggest widening the radius in which the bots will despawn and return to the player inventory.
The next biggest general gripe I have is that destroyed objects don't leave ghosts until you get regular bots researched. It would be nice to enable this from the start when this mod is active.