25% on AAdvantage might be worth more than 100% on BAEC -- check the miles needed to redeem the award you want. The earn/burn rates vary a lot by type of fare (as you found) and by type of award, so impossible to generalize what is best. But for low-fare travel AAdvantage is almost always the best plan. And splitting between multiple plans is generally the worst possible strategy for you (great for the airlines, you never redeem any miles). Also keep in mind that when you redeem an award, BAEC and QFF charge several hundred dollars more in "taxes" and fees than the equivalent Aadvantage award (e.g. an award economy SNN-BOS-SNN award on AA might have fees of USD 100 while BAEC and QFF would have fees of USD 300, typically). So it isn't just points that you need to consider these days.

Finally, the LONEx fare might have been cheaper than what she booked (and books into L class, also allows more flexibility as well as more travel).