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Machining Allowance is necessary if optimizing parts for Additive Manufacturing processes. After printing the part all functional surfaces are post processed. This is often done with milling processes. So the optimization actually needs to produce different outputs for different requirements

The optimization is carried out and calculated without taking the Machining Allowance into consideration to just have the finished design as part of the analysis.

So the MA is put on top of the design after the optimization step has taken place.