I'm not sure i'm following the two views you're trying to portray.
Basically, a fixed layout ePub is not just nice-to-have but absolutely necessary for some books! not long ago I encountered an educational book about electronics, it had hundreds of tables, formulas, lists etc... the kind of book you'd call a nightmare to convert.
The problem with having this book as a regular ePub is that when you have a huge table with lots of rows it will not fit to one page on an electronic reader, also it will change size depending on the font-size the user picks.
So in this case for example, a fixed layout would be ideal, because the entire table would fit in one page just like it does on the printed version and the user has the ability to zoom in.
As for conversion from ADOBE InDesign (use CS6), the options for conversion are pretty straight forward and should be pretty much the same for any ePub you're creating. The difference is, like I said before, is simply a few tags to add if you wish a book to be viewed as a fixed layout book.
Another great example for using fixed layout is this: (watch the video)
http://www.amazon.com/gp/feature.htm...d_i=1000729511
The lighting of different sections, the zooming etc changes the reading experience for the better, so fixed layout is really the only way to go in some cases in my opinion.