Thanks for the very handy tool!
I am using it to create old-school fps levels. So far the sectors work flawlessly but I had problems with the brushes. Something went wrong during build map so I had to reset the location, rotation and scale of every brush after finishing the layout. This way they did not get distorted during the build process. I leave this here in case somebody bumps into the same problem.
Edit: The problem came back so I looked into the python code. There are 2 functions which do some rounding. I changed both of them to round to 2 decimals instead of 1. This solved the geometry displacement for me.
Edit: I encountered another problem with substractive meshes. Sometimes they break the whole thing for some unknown reason. A simple substract window copy messed up the whole save file. I had to reload a previous state.