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I also make my plates 1/4" oversize so I have lots of margin while bracing and working on the plates. After the plates are glued on, I use a slightly under-flush bit in the "downhill" routing method shown in the diagram above. I found a bit and bearing combo that results in a very slight 1/32" rabbet for the flush cut. I like this because you can do the following sequence:
1) Flush cut the plates to be just under the side dimensions
2) Scrape and sand the sides to get them flat and ripple free. With the plates slightly recessed, this process is easier.
3) Then route the binding channels referencing the perfectly scraped sides.