Since station syncing was fixed (barring issues that have not been reported yet) dummy stations in between won't prevent stations from syncing anymore - i.e. it should work like in vanilla again.
In the current implementation, adjacent stations don't actually need to have the station starts next to each other, but for stations facing the same direction this is required for correct synchronisation to always occur - the adjacent station search starts from one station and searches for stations adjacent to the station start in both directions. So if all station starts are not aligned, which stations are synced will depend on which station is checked first.
For stations in opposite directions, as long as the station starts are next to part of the adjacent station, the rides will sync.
Combinations of adjacent rides in same and different directions work as you'd expect once you understand the above.
Whether this is how we want syncing to work is open for discussion. There are currently some aspects that could be refined/improved. For example, the rules related to the z height of adjacent stations requires all adjacent stations be equal height or height +/- 2 of each other. It might be nice if this height tolerance was applied from each adjacent station to the next so, for example, adjacent stations could be staggered down a mountain side. The z height variance allowed between adjacent stations also opens interesting questions about what should happen with stations stacked over one another?