1 Starting situation
To keep matters slightly simpler I have constructed a dead end street. From the bottom left the flanged track should turn into a normal track running to the top right.
The asphalt polygon is at height -0.15m, the grass around it at 0m. The subgrade section is at height 6.5m.
2 Placing tracks
From the bottom left I have placed the flanged track, following the street and thus at a height of -0.15:
From the other side the normal, S49 track will be placed, also at height -0.15:
The difficulty now is the connecting of the tracks, while there is a considerable height difference:
The flanged track has the railhead (top of the rails) at -0.15m, the "normal" railhead is at +0.25.
Of course, if this is just a short section that is enclosed anyway, then you can simply use polygons lowered by 0.4m as the "ground".
However when a longer track follows we have to change the height of the sub grade section from 6.5 to 6.1m:
We can now build the normal rails, using Z=+0.25, placing it parallel to the sub grade section (with distance 0 
Now we fill the gap, for this has to be turned on:
OK, in principle it works.... but well, look for yourself
3 Constructing the terrain neatly
First we lower the curb:
(I have disabled "Vertical adaptation at cutting" for the polygon so it doesn't follow the curb.)
I remove the middle curb section and place a "Transp./Cuts ground"-polygon with Z=6.1 and OFF:
Lastly I place the "curbstone_trackend_1" object (Streets and pavement elements). The snapping function (use Ctrl) can really help! 
should again be turned ON.
Done!
It does still look a bit rough but the ideas behind it should now be clear to you!
4 Bus/tram stops on traffic islands
When you are creating a traffic island to place a stop we can use polygons instead of sub grade elements. Using these polygons we can form the edges around the track:
The holes are then filled by splines or object that do not influence the terrain.
However it is crucial to recognize that in all cases, in case of doubt, it is better to cover the area of the transition with a purposefully constructed but completely static scenery object.
