Not sure if this matters, but it looks like you're putting the carrier on the edge of the light pad which has a slightly elevated surface. That could end up skewing perspective or focus slightly. Probably a much bigger problem if you were doing a smaller format though. Your stitching software may automatically adjust the perspective and DOF may be plenty on a large negative.
I would love to 3d print some carriers and masks for my CS-Lite light source but I don't have access to one. I've settled for cutting plastic with craft knives, using anti-newton-ring glass, or plastic slide mounts. This is for 35mm through 6x9.
Are you masking the light source? If not, you may end up with gradients on your images. It's a big problem for C-41 but not as bad for E-6 or B&W. I also like to put a lens hood above the negative, sized to rest on the carrier's corners.