If you have a craft that does not require a docking module to dock with a LM (e.g., three-seater, not sure if this also applies to the minishuttle), the docking step is rolled against the safety of the LM and not against the docking module. The relevant lines in the code appear to be:

I consider this to be a bug, with serious implications on the game balance. It means that if you fly Apollo/Soyuz, you can completely ditch all docking tests and rely on the R&D of your LM.