A rebuilt engine is only going to be as good as the skill of and care taken by the technician who does the work, plus the quality of the parts. If I had to pick one, I would prefer to take my chances on a dealer mechanic who (a) probably takes personal pride in his work (b) is directly identifiable as the guy who did it, if there are any problems, and (c) uses Factory Original parts. If, as I believe, the "factory remanufactured engines" are outsourced to the low bidder, that vendor is going to have to cut corners to be profitable at the low price. I don't know if they are obligated to use Factory Original parts or not.