Modular Pieces and lightmass problems, what is the best way to go?

The real fix today is to use the unofficial GPU Lightmass with proper lightmap UVs. Epic is working on integrating an even improved version of GPULM - the old Lightmass from UE3 that still ships with UE4 today is end-of-life and won’t be updated anymore. In the meantime, workaround as you did, or use GPULM.