It wouldn't remove 3 crossing sections (see bottom right) and ir probably decided to cross on the top left as opposed on the bottom right

I think so as well. There are 3 crossings either way, so the solver just picks one solution.

As a human you can look at the solution and decide it's not so pretty, but the question is how to model this as a general set of penalties. These also have to be linear - and if you have too many complex constraints, the solver may not finish in time.

Also, we see only a small part of the map. Outside this part there may be more crossings.

Yes, it would? One would just have to move the point where it splits in the bottom right a bit up.

Maybe it is the actual point where the track splits hence it can't be moved?

I thought about that later as well, but as the map isn’t exactly accurate, they could likely have moved it a tiny bit for that, too.