My dealings with AA have indicated that the first leg of the itinerary, and it's baggage fees, win. That does not apply if you have a coach only flight such as a regional jet and then a F/C ticket from there. But if your first segment has F/Y and you are in Y, then you pay baggage for full one-way as if all is in Y. You only get the F/J baggage allowance if you are in F/J on the first segment.
This may not be the *rule*, but it is my experience and what I had accepted as being the rule.
example: flying MIA-DFW-SEA over a year ago. DFW-SEA cleared to F upgrade but MIA-DFW not cleared as of check in time. Used only my normal EXP allowed baggage checked and not the F allowed checked bags (We had to re-allocate some items between bags since only 50lb limit vs 70lb limit for F). I just accepted that that was the rule (first segment defines benefits).