I found that flow incorrectly streams out GDS from DEF using KLayout. It implements incorrect DBU=0.005 defined in .lyt klayout technology file in PDK. Therefore, all sizes in GDS are 5 times smaller than in DEF. But sizes of merged STDcell topologies remains normal. In result we have the following GDS (spm design example). The DBU in .lyt must be 0.001!