I think we can access to the position number in Named BOM by using EPDM API.
Based on the event (pre-add, post add, pre-delete, post delete and so on) during which you would like to change the Named BOM and its position number, I think you will be able to accomplish you task if you follow \ try using below API interfaces and methods. Do let me know if you need any further help:
EdmBomCol_RefVariable (which can be position number, cutlength and so on)
Hope the above informaiton helps and all the best with your coding.