4) is not correct. There are 256 shades of grey, but much less height levels in game. Also some higher levels are flattened when you load heightmap but can be trraformed higher in game. I think it was discussed some time ago but no fix was done. As a goid test is to load a file with smooth gradient from black to white and see what happens.
I did not express correctly, I wanted to say the "Simutrans grey spectre/palette" that you should probably find on the forums or the maps website. I'll take a look in the code to try to find the correct numbers.
Which setting is meant to create half heights, 1 or 2?
(1) One, after all the other is a "double" height
I could be wrong, but you could test too.
So 1 pixel is 90m IRL (info from the data source website). This gives me area of 108kmx108km. However the tile size is set to 125m/tile which will ruin everything.
-Will the balance be broken (especially physics model)?
Well, the tile sizes in Simutrans are not realistic, as not all houses have a 125 m² terrain, nor buses are 125 m long.
About the height. I have a sea on the map so this will be level 0. If I understand correctly (and I assume that I manage to make it 90m/tile) this will let me have only 3 half-height levels?
The height is done by the shade of the grey used, you'll probably need to test to see if it looks like 145m or not.
Or would it be possible to scale the map in GIMP 2x and then I will get 45m/tile and 7 levels of half heights which should be awesome if possible.
If you are going to double the size of the file you can use nearest-neighbour interpolation. This will only make one pixel become a 2x2 pixel square without smoothing.