What I took away from this, and I only read OPs quotes, is that Allen was trying to make too many big plays. Which honestly seems like his m.o.
He has been learning to go with what the Defense gives him, he just need to do it more often.
I really feel, had he hit those shorter passes, they could have extended more drives, took more time off the clock and so on.
I have no doubt that this game will help him even more in making that adjustment, taking what is given and not trying to force it.