Make available in assembly mode the feature Merge - Inheritance and an option to set the level the feature must be created (assembly or part). There is already this kind of option when creating an extrude in assembly mode.
This functionality to select the level the feature must be created can also be added in the assembly feature Boolean Operations.
Maybe this new option can be available only with the option cut.
Today, Merge - Inheritance and Boolean operation can only be created at level part. Target is to cut several parts in one assembly removing volume of one additional part and to do it only at assembly level.