The Book panel was never designed for Alternate Layouts. When the engineers were working on that feature, they had a whole lot of stuff to add and that was not the priority. The priority was export for Adobe Digital Publishing Suite.
Why not break into two or three files which are shorter, with alternate layouts in each?
You mean, breaking the document into two or three files and then exporting each of these and then assembling the pdf files?
But then the hyperlinks from one doc to another don't work. I tried it already.
The problem is that I need to export ALL of these documents into ONE pdf because of the interactivity of the hyperlinks.