As far as i know, the STE in issue, repack, manufacture, transfer allow you to select BOM that you want to transfer and provide you with the list of item that you will transfer using that process.
The STE can also make material request if you need.
There are also some member in this forum @hiousi who made his manufacturing process based on stock entry, thus he created a custom module and custom javascript based on that, you might like to check it out…
