If your file contains items that are not supported in your required format (e.g. layers or 16 bits/channel) then the file format is moved to the Save a Copy command. This was driven by changes in the Mac Operating System, although the changes are applied to both Mac and Windows versions to keep them aligned.
In the case of PDF the format may or may not support all the content depending on the options you go on to choose in the PDF dialogue, e.g. downsampling, hence it is in Save a Copy.