I was almost sure that it wouldnt work.I could increase the footprint of the generators and/or decrease the build area of the Monolith, apart from that there's not much I can do about the positioning since it's not possible to choose build areas for different buildings to use.
however, decreasing the monolith build area sounds like an option. Necrons only have to build the 3 different core buildings and those are rather small. So it could be possible to prevent the building of gens within the monolith build area but still being able to build the cores. Combined with a reduction of the obelisk build area, so that you cant squeze to many gens around a single obelisk, would result in a more spread out generator build.