Looks like it understands the generated gcode, I could mill now my FreeCAD model with bCNC, all in Linux, thanks! There are still some minor problems with the z-coordinate, I want it to be at the top of my stock, but I can adjust this manually in bCNC.
One major problem: FreeCAD generated the command G20, which sets it to inch. So my 5 mm move in the gcode file, which was generated as FreeCAD would think it was mm, was a 5 inch move, which crashed the head into the top limiter. I changed it to G21 in the file, which sets it mm, and now it works.