You can try adjusting the "child component display when used as a subassembly" options on the subassemblies. In the subassembly configuration properties, you can change the the option to either show, hide or promote the child components. If you select show, the child components will be shown. If you select hide, they will not be shown (similar to marking each component excluded from BOM). If you select promote, the subasssembly itself will not be shown, and the child components will appear as though they are part of the parent assembly.
Worked like a charm, thank you for sharing your expertise!