I've done it both ways. If you are using Brunswick Super speed cushions the bottom glued edge will have a very slight amount of extra surface to glue up to. The draw back is that if you ever need to extract the captured nut plate you'll have to cut out or remove the plug.
Since I started using 3m 10 to attach the cushions to the rail liners, I haven't found it necessary to plug the slot. The bond is very solid and prevents the "thud" caused by early de-lamination of the cushions below the mortise in the liner face.
Jay