I think the interface does a good job of communicating to the player the assemblies that are needed for a job. I don't really see anything wrong with letting the players be responsible for constructing those nested assemblies. I feel that being able to keep these nested assemblies organized is what is going to separate the great manufactures from the poor ones.
I say this because the market costs & profits will be directly determined by how efficient a manufacturer is.
There are many 3rd party tools that are available to help organize manufacturing. (manufacturing calculators, open ERP databases, etc) that a player could utilize to give themselves a better understanding, and to develop a flattened or "summarized" BOM