Compound parts are only possible for the CAD geometry and should not be possible for the .stl geometry.
Merge parts is a feature that was created in the beginnings of the PrePoMax development. It is an opposite feature of the Convert element set to part feature. It is only meant to assign elements from two separate parts to one common part and does not change the mesh at all.
So for the functionality you need, new features would be needed. Something like Merge mesh and Split mesh.