There are multiple problems with the parts list and BOM, they are listed below and corresponding screen shots attached.
Issue 1: Rearranging items in a bom is a hassle, if a part needs to be moved from 2nd in line to 6th, the balloon does not update, you have to manually renumber. What would be nice is the bom linked to the tree, in the cases of multiple instances the first one the bom comes to, gives it a balloon. As you move that item up or down the tree the balloon changes. In a lot of cases a final BOM reflects the order I build the assembly, bigger parts first then to smaller parts and hardware. 90% of the bom could already be organized without even touching it. In the cases where it does work out, when turning on the structured bom, although the balloons are right, they are still out of order, requiring a re-sequence. If people don't care about the tree order, allow the BOM be the driving factor. Have a check box that tells it to ignore the tree order.
Issue 2: The parts list does not reflect the bom, the item I just moved in the parts list from 2 to 6 is still the second item in line. This means I am moving the item twice.
Issue 3: If a part is added and becomes item 7, if it is deleted (mistakenly placed), the correct part will come in as item 8, then you have to go back into the BOM and renumber.
These three issues are huge the bigger the assembly.