Any downside to booking airfare through AmEx Travel?

I've always booked directly, rather than with Orbitz, Booking.,com, etc. But is there any downside to booking through AmEx Travel vs. directly with the airline? My daughter needs to book a flight to Italy for a study abroad program and AmEx has a fare $100+ cheaper (the airline fare is listed, crossed out, with the lower fare below it, I assume some special AmEx deal). Other than noting that seat requests aren't guaranteed until they're passed on to the airline (which shows the same seats free, and plenty of others), I see nothing that concerns me - is there any downside?

And I was going to call about this, but as long as I'm typing... Does trip coverage vary based on whether I book with my card or her Companion Card? More generally, what's the required relationship between payment and passenger? If I purchased a flight on my card for my mother to visit, does she have the same trip/baggage/etc protection?