Merging selected part instances results in a new part instance and a new part. If you merge independent part instances, the resulting part instance is also independent. Similarly, if you merge dependent part instances, the resulting part instance is also dependent. Finally, if you merge a combination of independent and dependent part instances, the resulting part instance is dependent.
When you merge the meshes of meshed geometry and/or orphan mesh elements, the resulting part instance is always an orphan mesh part and it is always dependent. When you merge both the meshes and geometry of parts containing geometry and orphan mesh nodes and elements, the resulting part instance is a hybrid containing geometry and orphan nodes and elements, and it is always dependent.
Cutting the geometry of selected part instances also results in a new part instance and a new part. The discussion of merging the geometry of independent and dependent part instances applies to cutting the geometry of independent and dependent part instances; however, orphan mesh elements within a part instance cannot be cut or used to cut the geometry of another instance.