Most rooms do have dead spaces where the "age of air" is higher than the well-mixed parts of the room. So you can expect some of the room air to go through the filter more, and some less.
There are a few reasons this effect probably doesn't matter so much. First, the dead spaces tend to be places where people don't breath -- in closets, under furniture, in corners, near ceilings, etc. Second, where people do go, they bring thermal plumes and activity-generated eddies, which tend to mix up room air. In fact, the act of breathing also provides mechanical power that will promote mixing. The filter itself also blows air, giving more mixing than if the filter wasn't present.
The net effect is that the participating volumes of the room, where people tend to breath, probably get mixed at a rate similar to, or greater than, the rate at which the filter scrubs the air. Any non-participating volumes act as slow-filling and slow-releasing reservoirs, which delay the room's response to changes in outdoor concentrations.
I would worry more about the filter only cycling the air 4-5 times per hour. That's probably faster than the effective release rate of the indoor sources with which Mr. Hefferman (the expert cited in the NYTimes article) seems to have have experimented. However, it's the same order of magnitude at which outside air gets into most houses (especially in the parts of California affected by these fires). My gut feeling is that implies the filter isn't going to keep up so well -- though I'd want to model it to say anything definitive.