For the stacked there are three different types. One requires that you run one piece face up and the mating cut face down, the second runs both face up and the last (like the Freud offerings) runs both face down. For the first two you have more possibility for surface mismatch on the front of the doors. Also, with the first type the groove part is used for both cuts so it will wear faster.
Comparing to the matched sets, the stacked type can not be shimmed so once they are sharpened the fit of the joint will not be as tight.
I always recomend matched set, some people call a stacked bit as a one cutter that you just move up or down to get the job done.(just reset the height)
I see Bob and Rick like to use this type of bit and I'm not to sure why ,it may be because the Oak-Park setup you need to remove the fence to replace the bit .
If you use the matched set all you need to do is drop in the other cutter and the height should be dead on, that's if you use the rubber grommet in the router locking device.
The grommet lets/keeps the bit at the same height so you can make rail and stiles that come out true every time with little or no sanding them.
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