Since I started this thread, I figured I should continue to weigh in. Please note that I don't feel like I'm an expert in faction design in general or on this faction/unit specifically. Just giving my $0.02 - free advice and all that.
I still like the changes to the attack dice. More simple, still unique to this unit, less feeling of "this sucks" when opponent is rolling hot.
From what I can see, really the only thing we're gaining by having this flag option is to gain more mileage out of your command actions.
As Kevin stated, most of the time (80+% is my guess) you're just going to want to blaze away, friendly fire rules be damned. But there are times when friendly fire is a really bad thing, so we want to accommodate the player who wants to avoid shredding his own army.
But aren't there ways right now to stop it from shooting without using the flags?
You can Direct Control it and have it not fire (I always figured you could anyway in the current rules - maybe I was wrong about that). You can also have it move, since this unit can't move and shoot. You could also give it a different available target. All of these things cost 1 CA, same as changing a flag. The only lost benefit is that you will have to either spend that CA every turn or do something cute like give the battery a movement objective so it spends its time moving around. The flags let you stay put and extend that one spent CA for multiple turns and still be on the same target if it becomes available again.
I'm really on the side of less text = better when it comes down to it. You've already got one super wordy unit (Monks) and multiple faction abilities. Is it worth the added complexity to have the extra control on this unit? How often is it really going to matter? In both of our games, Mike set it to "fire and forget" and just played on and they did fine.
If you really wanted to grant more control using an established mechanism already in the design space, you could always add a "hold fire" checkbox that takes 1 CA to check and erases for free. I don't think that's nearly as complicated or wordy as the flag descriptions, but maybe I'm wrong. Because the checkbox is so familiar to BG, I don't think you'll have the "huh?" factor that Mike was just describing. I should add that as the opposing player, it was also hard for me to figure out which flag(s) were marked from across the table, and then what that combination of marks actually meant.
And to your earlier question about blue command cards, I don't think you need to add anything about that. I think there's already a precedent for "no cards when attacking" somewhere, and it makes enough sense. I was just being dense.
I guess I don't care too much about the short range thing, but again I'm not sure the payoff is worth the extra lines of text. It might make for more interesting tactical decisions about getting the unit up in someone's grill, but typically it's just going to sit in the back of the field shooting unless someone goes after it. So is short range going to come up that often? Does it really need it's own special set of rules for those rare times? Maybe. I'm undecided.
Anyway, tl;dnr Kevin does good work, and I certainly don't want to rock too many boats here. If it goes to print with the flags, I don't think it would be terrible.