In transaction CS14, we can compare BOMs. But in the initial screen, the primary BOM and secondary BOM are material BOMs by default.
Please go to the Goto->Primary/Secondary BOM Category in menu bar, here you can select different category for the two BOMs.
The categories can be chosen are: Material, Document, Equipment, Functional Location, Production Order, Sales Order and Project.
I also list some related notes for transaction CS14, BOM comparison.
2017544 – CS14: unable to navigate to primary BOM component if parameter effective change numbers are used.
1398101 – CS14: No search help (F4) on the change number field.
1875482 – Header of CS14 compare list can’t be exported to excel.
Hope this information is useful for you.