If I am understanding your problem correctly, you can publish PDF to a single file. In Organiser, create (or drag) a folder with the layouts you wish to publish into your publisher sets side, select the folder and change format to PDF, click on the "Merge to one PDF file" button.
A separate issue but slightly related, the "print entire layout book" option has gone, but you can select all the layouts you want and "print selected layouts" from the print dialogue.
HTH