It seems that the Wehrmacht would've discouraged this, what with experimenting with early camouflage patterns and blitz doctrines
It's about simplifying aircraft recognition. There are multiple cases from WW2 of aircraft being misidentified by friendly AA gunners on the ground, or by friendly aircraft, and being fired upon. Painting clearly visible markings on them makes it a lot simpler to identify a friendly aircraft. The black and white stripes painted on Allied aircraft for Normandy served a similar purpose.