I agree with you that we shouldn't put too much stock in these algorithms. Still, it's interesting that OK Cupid reached the same conclusion as Alex's wife: we're too different.
The enemy part is particularly interesting because it indicates conflict. The story would seem different if it was like "Ok cupid says we're 70% match but we think we're 99% match!". Instead, it's OKCupid saying: "you have conflicts" and the couple deciding to move forward despite those conflicts.
I'm not trying to make a big point here; I just find this part of the story fascinating.