On the other hand, I fail to see the argument for not extending the "plus" fare flexibility to the connecting itineraries which also have the inclusive bag and prices to match.

If anything, unlike non-stop where a ticket change will likely come from a change of plan or strategic choice to avoid booking a more expensive flight, in terms of connections, you may well have a flight that you cannot book because it is just below MCT (e.g. 55 minutes) but would easily make if your first flight is early. This could of course be restricted to people without checked luggage or could have a sufficient latest rebooking time to allow for the handling of checked luggage (just like flexible fares already do).