You should be able to contact AA and have the PNRs linked (not combined). Though technically I think that still means you pay the baggage fees for the domestic segment only since they are two tickets. I also think there is a decent chance an agent or manager at SJC would look at the total trip and check them in for free (especially since all the travel is on AA) - but YMMV.

Best bet is if you can get an email from AA ahead of time stating the bags would be checked without charge (even if the policy is otherwise, customer relations might look at the situation and see you are paying for an additional flight to use an award). Or if they reply back that you have to pay the domestic fee take your chance on a helpful agent at the airport.