Jon - I know the height of the shelf won't allow for a plate under the LiPo so if your cells do have bumps to locate in other types of chassis then they could cause a problem.
Rather than sand the cells - you could cut the shelf away and fit a carbon shelf that is slightly raised from the standard one - or if it is only marginal, take a sanding drum to the underside of the ESC shelf to 'gain' a bit of height.
HTH
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