Is there disadvantage in purchasing ticket from Expedia rather than AA.com?

I have multi city trip to Asia coming up. AA.com is no use in multi city. Google Flights can do multi city itinerary, send it to AA.com for purchase. But even Google Flights say to contact AA for purchasing when it comes to Premium Economy.

I called AA twice about Premium Economy on JL and CX flight, all on codeshare AA flight number. One agent even called a rate desk for assistance but no go, I mean AA is asking US$8,000 in Premium Economy and an agent said somehow it is pricing out using full Y fare. The rate desk could not do much better than an agent could.

Expedia can build itinerary I want on JL and CX flights, AA flight number code share, in Premium Economy. I only done dummy booking at Expedia, says it is Premium Economy and fare is $1,000 more than economy on same itinerary.

Is there any disadvantage purchasing from Expedia, or anything I should be aware about purchasing a ticket from Expedia not from AA.com?

If you must ask then my itinerary is:

JFK-(JL on AA flight number)-HND
HND-(JL on JL flight number)-BKK
BKK-(CX on AA flight number)- HKG
HKG-(CX on AA flight number)- JFK

BKK-HKG flight does not have Premium Economy, so it is in economy. All other flights are in Premium Economy according to Expedia and fare is $1000 more than economy in exactly same itinerary.