I think the rules + FAQ as written create a contradiction here and I'm trying to make sense of it. My position is developing as I work my way through this. I agree that my logic there is flawed for the reasons you spell out. However, the logical conclusion of that same interpretation is that Howlrunner could grant a ship attacking Omega Leader a re-roll since the ability to modify the attack dice originates from Howlrunner and not the attacking ship. I don't think that was the intention of the FAQ ruling. If it is, then it really needs to be rewritten to make that explicit. If not, then it needs to be rewritten to clarify what's actually going on.
I think the confusing element here is that M9-G8 can function both as a "Defender Modifies Attack Dice" and an "Attacker Modifies Attack Dice" ability, but the origin of the ability is from a ship that can be the attacker, the defender and also neither the attacker nor the defender. Since it doesn't fit neatly into these categories, it is difficult to extrapolate how it should interact with the current rules + FAQ.
I think you have locked into the main problem here.
Through the Omega Leader ruling with Elusiveness and R7, FFG made a distinction on the source of modifications.
With Snap Shot, you can carry that ruling over so that the equipped ship may not be able to modify, but if the source of modification is external, it's allowed.
It does bring into question M9-G8 and Jonus on whether they will provide for a reroll or not.
Edited by USCGrad90