In my experience, tracks and paths follow different rules. Track limitations can be turned off (partially) but not path limitations. The upshot is the following 3 bullet points:
* a station (but not the rest of the track) must have at least 4m clearance above or below any existing path.
* a path must have at least 4m clearance above or below any existing track, and 4m below and 8m above an existing station.
* a track (not the station, just the track) can be placed at any elevation relative to an existing path.
So, if you want tracks making level crossings with paths, or running along main street paths at ground level, you have to make the paths first. If you also want the station at the same ground-level elevation as the track and paths, you have to leave a space in the path network for the station, so you can put it at ground level. If you have to change a path at the same elevation as a track, you have to delete the track first, then change the path, then rebuild the track there.
Note that stations have a flat surface bottom that's 2m below the level of the platform. It's this flat bottom that must be 4m above any existing ground-level path, so the track in the station is 6m above the path.
