Thanks @firstdefence and @Dan C for your comments. This is very helpful. I've been playing around with the book feature as well as the autoflow with picture frames to see if I could come up with a workflow that was at least better than what we currently do via MS Word. What I found is the following and please correct me if I'm mistaken as I only spent so much time play around.
1) The book feature is nice except that you seem to have to manage your master page(s) in each file you've made a chapter rather than being able to apply a single master to the entire book. So if you applied that concept to importing PDFs as chapters and wanted a header and footer on each page of this combined document you would have to do that for each file. That's not worth it. We're often working with 40-50 PDFs. If the book were able to have masters that could be applied to each chapter that would do the trick. I think that if the feature allowed the user to override all masters in a selected chapter with a book master that would be ideal as it would provide options for how to work. If you need the granularity of many masters you simply do it in each chapter file but if you want a unified look across the entire book or for a specific chapter you could make that happen too. Im my case, assuming PDFs were supported, I would only need to use the book masters across each chapter.
2) Using autoflow with picture frames seems to work pretty well, although while testing this Publisher had to be force quit a few times when trying to Place a PDF. It simply became unresponsive for a long time.
Linking the PDF files does allow for updating any changes to the PDFs however that seems to be with some limitations. If I changed the number of pages in the PDF Publisher did not like that. Deleting a page from the PDF file and updating made it duplicate what was the new last page in the PDF so it occupied the same number of frames. Adding a page to the PDF did nothing. I also got unpredictable results trying to replace the asset via the Asset Manager. Sometimes it worked sometimes not and the number of pages was an issue here too. It had to be the same as what there was previously as far as I could tell.
On a final note, I noticed that autoflow will overwrite existing content in a frame. The conditions were that I wanted to insert a multi-page PDF between other pages that already had their frames filled. If I did not insert the correct number of blank pages with frames autoflow would simply continue through the already set frames. Autoflow needs an option by which it will not overwrite what is already in a frame when you are inserting a multi-page PDF or set of images in the middle of a document. Much like it will automatically add pages with frames at the end of a document if you don't have enough to support what it's inserting, it should be able to do the same mid document if you want it to.
Thanks!