The treaty says that sepultures should be kept with dignity but makes no mention of the color. At the end of the war, France ended up with a massive amount of dead Germans on its grounds. Being on the winning side they refused to return the bodies saying they came here to die and they'll remain here. Unfortunately, in the aftermath of the war, esthetics of the vanquished cemeteries was not a priority. So they went for the most durable artefact, wooden cross covered in tar to preserve it, hence the black.

After the signature of the treaty and seeing German cemeteries on French soil becoming a reality, Germany created the Volksbund Deutsche Kriegsgräberfürsorge (VDK). They finally got access to said cemeteries in 1926, as they were not allowed to enter France yet. By that time, French government realized they couldn't follow with maintaining the sepultures anymore. Local population did not appreciate German presence, even dead, and were prompt to destroy it. They were degrading fast.

VDK then called an architect, Robert Tischler, to "design" the cemeteries. Being a veteran, heavily traumatized by his time there, he chose to give as guidelines a gloomy feel. He kept the black cross and forbid personal messages to maintain brotherhood in death (only name, rank and regiment). The trees were to be planted more or less randomly and never be trimmed (complete opposite to French military cemetery) to maintain desolate aspect.

In 1966 a new agreement was reached in the wake of European union as to the management of the cemeteries and wooden crosses were replaced by black metal crosses.

To understand the massive task of VDK, remember that by the end of ww1 there was 1 937 000 German bodies in 28 countries. 750 000 more after ww2.