If this process satisfies, you can use FIFO method also. I used this method. I set negative line in BOM and it scrap item will be in production journal. When you post item negative consumption, never mind what method is set on them. Cost will be allocated only on output line, not for consumption line.
You have to be careful to never post some cost to tghe this scpar item (from purchase e.g.). If you do that, then you will get cost more then 0,00.