The configuration of the BOM line depends what you need of course. If you need it to be a reference production order when it is a BOM line then the line type must be pegged supply. The reference level being zero is not really relevant to your question, the reference list shows referenced orders. Orders created by planning are not reference orders unless you configure them to be. The zero may impact on the reference list, my point is that just because planning creates the order that does not mean it is a reference order which is different functionality in AX.
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