You can have several alternative BOM. But if the Manufacturing order is created automatic (MTO or Scheduling job), it go right into status Confirmed.  Then you cannot change bom.  The top bom will be used.  A trick to avoid confirmation is that the top bom does not have components, That will avoid the manufacturing order to be confirmed, and you must choose a bom or add components. (A manufacturing order must have components).

An option is to add a component and set the requirement of the original component = 0.  That also works fine.  Be aware that if you use work center / work orders, the status must be Unplanned.