You'll be able to tweak the sizes in openscad, somewhere in the scad file there'll be a line that cuts out the hole, and you just need to make that number smaller. If it were me though, I'd print out a thin-walled hexagon shape that the 1/4 nut fits into, with the same outer dimensions as an m8 nut, then glue the 1/4 nut inside. It'd be a lot less printing, and you can keep the modded nuts if you change x-ends at any point, without having to modify the design.