The documentation on this functionality is indeed lacking. We plan to improve this and have the work tracked internally. Although this is a valid issue, we do not track documentation improvements via this channel.

As for the comment about alpha clipping "not working as intended because any calculation inside the shader is being ignored", while this is true, it isn't unintended behavior. The lightmapper supports transparency by generating its own set of transparency textures, based on the material inputs. This is done in order to avoid having to evaluate arbitrary user shaders during baking. Thus, it only supports a limited form of transparency. We'd like to make this behavior more clear and intuitive to use in the future, and we may for example expand the MetaPass (which is invoked just before baking) to also render out alpha, but we have no intention of ever evaluating user shaders during the bake process itself.