I think the conventional wisdom is that the programmed engine will not be able to outplay a top-tier human engine builder like jonts. Although you can include some tricks like filtering over Estates with Courtyard, there will be other subtleties (reshuffle, etc) which are harder to code in.
On the other hand, I think it IS true that a programmed BM strategy will be able to simulate a reasonably good BM player (what the simulator lacks in decision making power, it can make up for by tuning the parameters a bit smarter). The fact that the programmed engine is able to beat the programmed BM is very suggestive to me. If you're talking engine versus engine-BM hybrid, well, that's a different story.
I still agree with Stef that for average players, even for top-tier players, BM is safer than engine just because engine is trickier to set up and requires much more skill to execute.
WW, in the two games you cited against jonts, one ended on piles and the other ended in 21 turns.