Conclusion and new Hypothesis
I think I know why exchanging the river MOS files for renamed grass files produced the result without the black textures, and why rebuilding the river MOS files did not produce the desired result.
While tinkering with the MOSEditor and the MOS files, I noticed that when loading an existing MOS file into the editor it would also try to load the corresponding textures, and produce errors if I didn´t point the editor to the locations of the dds files beforehand.
It seems that the purpose oft he Editor is to create a MOS file, that will blend multiple texture files and their ALPHA masks. What the Edior does not do, is to define the properties of the texture files, like for example glossines, reflectiveness, etc.
The renamed wildgrass MOS file was able to produce the result without black textures, because it was still calling on the wildgrass dds texture file, instead of the river texture file.
New theory: I need to find the files in which the game defines how a texture will be rendered in the game.
How does it work with aircraft? Where are properties such as glossines and reflectiveness of the surface textures defined?