1. On the scale of "the whole map", going around a city isn't that much of a detour. You only need local authority permission for stations or bulldozing city buildings/roads, so build stations first the rail around obstacles.

2. Forestation projects are an easy way to build local authority rep. There's also a floor to how low rep can go, so if you need to bulldoze a forest to make room for your reforestation project, that still works out