Another factor is downfield blocking. Did people notice that on Allen's 40 yard TD run as he broke into the open the new WR Cooks blocked his cover guy all the way into the end zone.
In Ohio they broadcast the High School football championship games live (7 division so 7 games over a 3 day period) and I remember him QBing a small HS having an amazing game in a tight loss. I remember thinking that I had never seen a HS school kid with so much zip AND accuracy on his throws.
You are right, the O line and Cook are elite. But if they didn't have Allen and even with a star DE as a result of the CAP savings, the Bills are a 500 team.
To be fair I think not having Bishop on the field for that drive was the main cause of this. Bishop has improved so much and is playing at such a high level that having him out of the lineup for that one drive was very noticeable.
This is a fair question and points to the defensive game plan preparation. There is no doubt that in most of the Bills games this season - wins or losses - the D plays much better in the 2nd half. They need to fix this or thy will be one and done in the playoffs.