I don't know how helpful this will be but I'll tell you how we look at scrap and yield, particularly with the steel we use.
 
Yield is the number of parts we can get per pound of material assuming all parts are good.  There is no built-in scrap factor.
 
Scrap, to us, is bad parts - parts that cannot be used.  These we handle by issuing material to the work order under WO-G to reflect the amount scrapped.  So if 3% of the parts are found to be defective, we would issue the equivalent quantity of raw material to the job and not enter finished production on the bad parts.  In therory, this accounts for all material.
 
Quite often we will adjust the lot size of a work order to reflect a variation in the raw material on hand.  In your case, we would not want to trigger a re-order for 1000 lbs. of material when we are only short 50 lbs.
 
We "cover" scrap by ordering slightly more material than is needed for a job.  If it ends up sitting on the rack, fine, we'll use it on the next job or over-run slightly.
 
We are not a job-shop so we have the luxury of doing this.

If you entered a scrap % in BM-A, you can globally change the field BKBM_PROD_SCRAP in the file BKBMMSTR to Zero.
 
I guess you still have the issue of ordering "extra" material to cover scrap.  If it is a known amount, you could cover it in the yield.