The SCI group is still very much active but it is true that not much development is going on for this particular project recently. My understanding is that they are still committed to maintaining their software and Kitware helps them in this, too. Latest release is 3 months old, so it is not too bad.
Can you show examples? You should be able to resolve this, but you may need to increase the resolution of the mesh near boundaries. Cleaver is intended for biomedical applications, so it may smoothen sharp edges, and where multiple materials meet, sharp edges are inevitable. Also check out how the input segmentation looked like. There might have been 1-2 empty voxels at the junction point.
See this page: GitHub - lassoan/SlicerSegmentMesher: Create volumetric mesh from segmentation using Cleaver2 or TetGen
The main difference is that scale essentially specifies how densely the input is sampled (if you take few samples from the mesh then execution will be faster but you will lose lots of details), while multiplier controls element size (if you have large elements then you will have a simpler mesh but cannot represent small details).