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I like your reasoning, and I think that must be it. I had assumed the OE rating had already taken into account the garbage drives based on this quote from the page,
Based on that, I had just assumed the garbage drives were never considered. It would definitely help things make more sense if that were not the case.
There is a lot to how Football Outsiders massages the data. A lot is throwing out garbage time as already pointed out by @AE 87. But there is a lot more. The book "Study Hall" gets into some depth. They also estimate the value of every play by measuring the difference in point value for the starting yard line and ending yard line of each play. (Every yard line has a point value associated with it.)
Given the limited statistics that are collected for college football games, they had to go back and regrade every play for select games. So they do a lot of stuff that we don't see. Better descriptions may be on the Football Study Hall site or the Football Outsiders site, I just haven't looked enough to know.