We ran a cost roll up based on standard cost for all Bills and did not check the "update intermediate bills".  This showed only a few bills that had any variance.

Then we ran a cost roll up based on standard cost for all bills and checked the "update intermediate bills".  This showed variance on a large number of bills, including many of the top level bills.  We also saw that it did a cost on phantom bills as well, even though phantom bills are not items and do not have any cost associated with them.

This led to questions as to how cost roll up calculates the cost, based on both the "update intermediate bills" being checked, and based on how the top level bill is built (with or without phantom boms).