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For the OP, I have both l-plates for the 5D markII, battery grip BG-E6 as well (Canon not aftermarket). I recently went to using only the l-plate and body, with out the battery grip after a long time of using battery grips with previous cameras.
I personally found that with the battery grip and l-plate, the camera felt very stable. I only removed it due to added size and downgrading to a smaller bag (Retrospective 20) from a Domke J1. Also note that while the battery grip is held by the tripod screw, it does have a larger base than a smaller quick release tripod base. Also the same goes to the RRS l-plate as it's a very large base and feels very stable.
As for the overall comfort, I never had any issues with my l-plate on a battery gripped body. The plate is contoured by the bottom, and the only part that stands out is the vertical bevel area which is in front of the ports. So technically, you will not place your hands on the corners in normal use.
But with the battery grip and l-plate, there is added bulk. Keep in mind, as it won't fit in any bag that is already a tight fit without a l-plate.