Just an idea. Instead of doing a 2-layer BOM, maybe just add container to the master BOM as a component, and set it to be backflushed, so that it can be auto consumed when you close the WO. 

We are a chemical batch manufacturer.  We sell same product in many container sizes.  We package product at time of mfg so we do not stock "bulk" product in X3.  The way we handle this in X3 is our master BOM (raw materials only) is setup as a phantom product (we call it a base) in X3 (this is an out-of-box product category).   Then we setup each container size as a separate part number (finished product that is sold).  The BOM with the container has 2 lines- one for the phantom product (base) and one for the container.  We have used X3 for 15 years and this works well for us.  You can even combine multiple finished products (like different container sizes) on a single WO.  Since the base product is not inventoried - it does not require a lot number.

We are a chemical batch manufacturer.  We sell same product in many container sizes.  We package product at time of mfg so we do not stock "bulk" product in X3.  The way we handle this in X3 is our master BOM (raw materials only) is setup as a phantom product (we call it a base) in X3 (this is an out-of-box product category).   Then we setup each container size as a separate part number (finished product that is sold).  The BOM with the container has 2 lines- one for the phantom product (base) and one for the container.  We have used X3 for 15 years and this works well for us.  You can even combine multiple finished products (like different container sizes) on a single WO.  Since the base product is not inventoried - it does not require a lot number.

Thank you, Jeremy.  This sounds interesting too and will test it.