InDesign. It's been the industry standard since Quark fell out of favor (although it's still around).
Although Quark still loads data from external sources and will work with FileMaker via ODBC.
If you're looking for an alternative to InDesign, then Quark is probably the next place to look.
InDesign and FileMaker Pro are both AppleScriptable. You can automate complex workflows, reducing the workload to a few mouse clicks.
caveat: my publishing could be characterized as "vanity-publishing". Anyhoo, I wrote a FM program to create Sudoku puzzles. Then I adjusted it to create entire books. (I also used FM to design the covers).
So, my perspective on your question ... I used FM to create a group of .pdf files. Then I used an Adobe product, Acrobat Pro, to compile the entire project and add page numbers. I don't know if that's a sufficient platform for you.
I second FMP and InDesign, as well as add Photoshop and Illustrator. Applescript is the magic that lets them work together and makes automated workflows possible, dependable, and efficient.