Altug thanks for the lengthy explanation - Just experimenting -
You probably know most of what I have written but may be useful for others.
I converted your static S3D boat to buoy file with Object Editor.
Not sure if you have tried it as buoy file.
Sank like a stone with the default Object Editor Settings but if you alter the mass in main box (Object/Frame Properties) to about 10,000 it will float, then save and export to Scenery Designer.
The XYZ settings to adjust the angle it floats at, if needed.
I also optimised it in Object Editor but not sure if you need to.
Would still them need to add the collision spheres and use the text editor (fix) to get them to work.
I think it is about 30,000 faces in Object Editor and Stentec's static "buoy" boats are around 1,500.
I kept mine I think to around 1,200 to 2,500.
Alex's trees are about 300 faces each I think in Object Editor as are solid with some transparency I think, made from the 2 interleaved flat planes.
With the 32 bit alpha file these would be 2 polys for a flat side of 2 triangles I think, maybe 4 if double sided and 8 for 2 interleaved planes to make a small tree. The catch being though it will only work in Motorboat 1.2 version as its a new function Stentec have addded. But it would mean you could create very interesting coastal scenery with very little cost to the frame rates.
Suspension bridge sides, any skyline of buildings, mountains, tress, forests, vegetation, river banks, cities, individual trees woods, and forests. Also ships rigging, the spokes on the wheels of carts, etc. The list could be endless.
Regarding the vrml file not sure if you you used vrml2.
I don't think vrml1 works.
Thanks for the info on what the different setting do for and will have an experiment with them.
I don't know why Stentec didn't explain these things as they are essential for model making.
I use gmax for creating drivable boats (on fixed track) and dockside items for a train simulator.
Gmax is free but can only be used if Stentec get a commercial licence for a plug-in to use it, and can't see that happeneing anytime soon. Its easy to get a nice smooth looking appearance in gmax by altering the smooth settings up to 180 degrees on boats hulls.
To keep polygon counts low handrails etc need to be just 6 sides, etc on cylinders. Same with funnels, etc.maybe 8 sides for funnels? The more curves the higher the polygon count and lower the frame rates.
Drivable boats you can go higher but thats something apparently in the distant future for our own made boats.
Just discovered the canal you made on your route and like it.
That is my interest on the routes like Ellesmere Port, etc.
In the train sim a working lock has been made by 3rd party and the water will rise to next level and gates open etc.
However that is using fixed track for the boat and a flat plane for the lock water.
managed to make a horse to tow and connect to my narrowboats along the canals in the train sim but getting the legs to animate on the horse too difficult in gmax for me at present. I dont think it can be done at present in the sail or m/b sim as one water level.
You could attach the horse to the horse model offset to be over the canal bank towpath but water would have to be without waves.
But again not much point in trying if we can't move our own made boats.
Found I can save the files in Blender I make for the Stentec sims to DXF instead of vrml2 so can also then use them in the train sim after converting them..after importing them into gmax.
The seperate forums for the motorboat and sailsim don't seem very realistic.
I will be use static floating steamers and sailing ships in the sail sim and will be using static and drivable (if they become possible), sailing ships, square riggers and side wheel paddle steamers in the m/b sim.
Mind you I also use mainly my own drivable sailing barges, steam barges and narrowboats in the train simulator.
Barry
Addition ..Tried the lighthouse I made with the emissive settings altered to 1. It has a seperate window for the lamp room so just the window can be altered. Shows up fine at night time now. Still can't get it smooth though with a texture in Blender. The static steamer has seperate semi-transparent windows not attached and lights up if I set the emissives to 1 for the windows . Can put lights on any future boats now as long as I don't attach them in Blender and perhaps a few houses with lit windows. Will experiment further.
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.....Let me know please....
I am just downloading MBS 1 even without the patch 1.1.2 and forget the new version 
transparent water surface