Whenever I use GMSH in SALOME I never had the problem of these edges, only when using NETGEN (if I recall correctly from my geometry) I also preffered GMSH over NETGEN as I could give the maximum element size and it would not cross over between surfaces as it would with NETGEN (but that is probably fixable, but out of the box I liked GMSH more). Not sure about the performance hit. But you can just mesh with GMSH even outside of SALOME if you really would like right (not sure about STEP input/read)?