I use RRS L-brackets, but can probably answer. The differences are very small and probably don't matter in many cases.
RRS says it is better to use RRS brackets with the RRS lever release since there is little room for adjustment to accomodate small differences in clamp groove design. With the regular screw release it does not make any real difference. This may just be sales spin since Markins does not have a similar requirement on their new lever release.
Another factor is the Kirk is often a little cheaper by $10.
These are custom designed items. There can be small differences in features and access to the areas on the side of the camera. The Kirk bracket on the D70 allowed a little easier access to the flap on the side. Another example - the D300 L-bracket from RRS had a slot rather than a single screw hole to allow small differences in positioning. The Kirk model (I think) had a single screw hole allowing no variation.
And of course, buying the Kirk models through the Pro Shop helps support Nikonians.
For more thoughts and discussion you might want to post in the tripod and support forum