I think there are quite a few different concepts mixing here.
First thing that is sorely lacking in AE, especially in worlds starting before the '80s is second freedom (stop in a foreign country for refuel and/or to unload pax, aka "direct flights"). This would tremendously help early on in those worlds, would allow a relatively painless (eg non-game breaking) introduction of the whole itinerary concept, would allow plenty of space for fine tune and general feedback whether the players like it or not. Making pax decisions whether to take a non-stop or a direct flight is an easy flight time vs price equation. IF there is competition. A good second freedom example is QF SYD-LAX-JFK (dropping off pax in both LAX and JFK but no LAX-JFK service).
Sorry to nitpick but it's a BNE-LAX-JFK route
but because BNE-LAX is 6x weekly, SYD picks up the Monday flight. Also, it would require a huuuge amount of data collecting to implement 2nd freedom flights, and i get a feeling some countries, you won't be ablt o find such old documents. Also i think Yuxi doesn't want to like say in a world going from 1960-2010. countries will eventually not renew 2nd freedom flights to particular airlines, so he'd have to change the political restrictions for every country countless times over the course of 1 world. Also, say i'm running a route that goes from Country A - Country B - Country C - Country D. it is now 1980, and country B doesn't let me fly from B-C anymore. so then you'd have to reroute the aircraft again. Basically, 2nd freedoms would be a pain in the back to implement. Alternative is O worlds
Fifth freedom (flight originating in own country, landing in country A and then country B while transporting pax A- should NOT be made available because it's impossible to make it fair to everyone. There simply is no system that could make fair. An example would be LH FRA-BKK-KUL where you can buy tickets for BKK-KUL alone.
Again, pain in the back. Requires lots of data collecting, and runs into the same problems as before if a country doesn't allow 5th freedoms.
As for sixth freedom (transport pax between countries A and C via own country B, aka hub networks) also opens a whole can of worms. Pax decision to take a route should be based on both total time, price and IFS (especially premium classes) but for time you need scheduling, for that you need slot realistic management, and that won't happen without an economy overhaul. Price is also a problem because so many people dumping capacity mindlessly on routes (also there are lots of "life support airlines" operating at zero profit or less); excess demand generation is favoring the dumping airline; and in general the numbers are waaaay off (Bristol-Sana'a 2F 18C 99Y daily? Seriously?).
The configuration problem has been raised '000s of times. the only way to rectify this would be increase min. pitch for F and J/C.