The part off diameter is how deep the the machine will carve at the ends. It is how much dowel will be left like big tabs. There are "forbidden" zones at the ends of the virtual dowel in Designer. I think that if the part off (or any part of the pattern) is in these zones, it does not carve it. If your dowel had been longer in Designer, the part offs would have been out of these zones and the machine would have plunged down deep at each end to carve them.
Look closely at the dowel in Designer and see the difference changing the part off diameter makes. I think you got lucky here and avoided disaster.