So the new free roam lets you place stop marker, of which when arriving at you gain a significant number of points (more than the drive mileage one) my suggestion is to remove the ability to earn points from the free roam stop marker (the one players can set for custom paths) as it will become an easy exploit for AP points, as all you have to do is move it slightly ahead of your train and stop or perhaps on top of it, to achieve such points. I think this currently detracts from the value of earning AP points at this current format and would make continuous fair gameplay of all players in this respect redundant.
Luckily points are meaningless and so it is also meaningless to cheat to gain more. If players want to add multiple waypoints and keep endlessly adding destinations in order to get more points then all power to them as it will be a tedious and unrewarding experience for no reward. Let them have their cheat points as they won’t be having a good time getting them and they can’t do anything with them once they have them.
There are much easier ways of farming points if that's your thing. Simply do a large senario or service, save just before the end and then finish. Once you have the points, reload the save and repeat. You get the full points each time! You're only cheating yourself and your points and level become meanness if you farm points in this way. Don't even get me started on how easy it is to cheat with Mastery, but this is a great way to get back those levels I lost having to restart from zero when switching to the PS5 version of TSW2 as there was no profile transfer!