Since 22.4, if your file contains items that are not supported in your required format (e.g. layers or 16 bits/channel or hidden pixels etc) then the file format is moved from Save As (Shift+Ctrl+S) to the Save a Copy command (Alt+Ctrl+S). 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 it will appear in Save a Copy as the dialogues that follow the choice of the PDF format, allow elements of the file to be lost (e.g. downsampling or not keeping editability). So it is in the Save a Copy category.
In 22.4.2 two new options were added to Preferences > File Handling. The first allows you to revert to the legacy Save As workflow and the second to optionally omit the word "copy" from the filename when using Save a Copy
In my opinion the Image Processor Pro plug-in is better than Adobe "Save a Copy" feature. Save a Copy can ovewrite a copy. Image Processor pro would not do that it will create a new version not overwite a previous version.