I'm not so sure about the upgrading thing. PE is a product created to generate revenue from those who can't buy J either for corporate travel policy reasons, or personal budgetary, but could afford a small premium over regular economy. Why would AA, or any airline offering a true PE product, give it away with advance upgrade options? Remember that upgrades are tightly controlled, it is more likely the larger capacity J cabins will still have empty seats, while the objective of PE is to sell every seat. That would suggest to me that SWU or miles upgrades would still be from Y to J for a while longer, at least until the fleet has been at least 50% or more converted.
AA has already annoyed we ExecPlats by reducing the number of SWUs we get. And increasingly advance confirmation of SWU upgrades on overseas flights is becoming a thing of the past, clearing a day or two prior to flights, or at the gate. To limit them to "next cabin" on flights with PE would severely reduce the number of open seats by flight day, while there could be many more open J seats going out empty. And every PE seat taken with a SWU upgrade means AA doesn't get the enhanced revenue it's after.
It would be in AA's interest to modify the wording for this transitional period as cabins are reconfigured, and specify Y>J or J>F on such aircraft, and perhaps offer ExecPlats comp upgrades to any empty PE seats at the gate. BA often upgrades its Gold and even OW Emeralds from World Traveler to WT+ on a comp basis when there are open WT+ seats. I an see AA doing this, not guaranteed but as a courtesy every so often, until it comes up with new SWU policy, or even an upgrade credits system ala Air Canada.