I think for the free luggage section it is a fair one and kind of same as current arrangement

The first case assume it is on 2 different ticket (as said, "Each Purchased Ticket"), e.g. travel on J on JFK - HKG then Y from HKG - MNL, which for the HKG - MNL it is definite that they can charge you (currently its kind of blur / grey area ? )

For the second case it's kind of voluntary downgrade when no F / J seats are avaliable (such as domestic connection on AA / JL) which is what always been doing. Last time when I travel on a open jaw J award trip with JAL Y in the middle I still get 30KG for the JAL Y flight.