Yes, now there's an option to Merge BOM. There are typically two reasons why:
1. Some users haven't built all their components yet (using Build Part) so they will merge later (using menu: Assembly / Merge External BOM...)
2. Some users wanted to verify if the BOM was accurate with the existing PCB design - if there are any missing components, or different part numbers used, FAB 3000 will pinpoint those locations.