Without using the Site feature, what is the best way to manage a BOM that has one different line item for different manufactuing location?
You can use a new attribute on the BOM table of an item named Site and linked to the dynamic list of Sites.
In this way you can specify if the item is site specific or not. The feature of site specific offer a lot of other things that you will not have doing in this way but releasing an item as site specific is an irreversible process.