This is a simple way to generate custom tiles for a multiboard. A simple rectangle multiboard tile generator, where the sizes and a hole can be specified.
Another way is to create a new OpenSCAD file and look at the CustomBoardExample.scad. This is a way to create any shape necessary to accommodate your needs.

These files needs the original tile components from multiboard. Because of licenses issues I can't distribute them with the rest, but they can be downloaded at https://than.gs/m/994663. When the stls are besides the OpenSCAD script they should be found automatically.