I don't think it was a robber concept (man coverage with one deep safety and one safety in the shallow middle of the field) but a zone coverage when they were expecting man. In that case it wouldn't have mattered if Gronk was running in place of Allen.
They definitely looked like they were in man before the snap and switched, but Allen was open on the seam if Brady had recognized what they were doing sooner. Generally, the corner playing off Hogan would drive hard upfield on that throw in man, while the slot corner would cover the seam. They were in a cover 1 look, but the single high moved toward the twins side on the snap, as did the linebacker on that side (to cover a possible double move back inside by Hogan or the slot receiver if he broke inside off the line).
They were able to run this because the Patriots decided to spread the field side with two receivers and they didn't have to worry about the boundary side much beyond check downs or crosses, which they had covered.
So I think Brady was expecting man, saw zone when the corner came off Allen and short armed his throw a bit. I think Allen being in the slot was part of why the corner left that route so early. Allen was open for an easy 8 or 9 yard gain and Brady usually hits Gronk on that. I don't think the coverage would have changed if Gronk had been in the slot, but I do think the corner would have carried that seam another step or so before breaking on the out route, or at least kept more balanced leverage on it instead of immediately jumping outside of it.
So I think it was just a perfect storm of a great call, Allen being the slot receiver and Brady getting fooled but seeing it late, which drove the throw inside. If he had let the throw trail to the sideline, Hogan has a chance to make a catch and at least the ball won't be intercepted.
Edit: Brady also had the drag route open slightly, but that was clearly not his first or second read. It would have taken a good move to get the first down, but it was open. The sit down route on the backside was open, too, but again, that's not even close to his first read in that look and is essentially a check down. It also wasn't *that* open, but enough to get the ball there with a tiny bit of room to wiggle.
It was ironically a really safe play call by the Patriots. High chance of a completion generally.