You can make a single part out of 2 or more parts that have overlapping geometry and are of the same material. The merged part can be edited to add or remove parts.
Part panel
(Merge Parts).
Part panel
(Edit Merged).
Merged Parts panel
(Add) or
(Remove), and then select the parts to be added or removed.
(Finish Edit Mode).
Part panel
(Edit Merged).
Merged Parts panel
(Add) or
(Remove), and then select the parts to be added or removed.
(Finish Edit Mode).