Moving to InDesign EPUB forum.
It's definitely not possible in InDesign. I doubt that you can do that, but I'll leave that to the EPUB experts here.
I asked Joshua Tallent of eBook Architects this question – he's one of the great experts on ePub – this is his reply:
"Unfortunately, there is no tool that can do that. Additionally, while that is technically possible in EPUB 3 to have both reflowable and FXL renditions in the same package, I am not aware of any reading systems where it is currently supported. It is best to stick with the simple solutions. Make reflowable if you can and sell that everywhere. If you do make Fixed Layout, that works best in iBooks."
Many of Apple's exemplary ebooks are (or at least were) such combinations of a flowing and fixed content. Such iBook files are not called .epub, but they sure are based on ePub standards. You can view them in on your iPad in iBooks in 'normal' (fixed layout) mode, or switch on the scroll (reflow) mode. In earlier versions of iBooks, this switch was triggered by using the landscape or portrait orientation of the iPad. You can create them in iBooks Author on the Mac (Pages only plays nice with reflowable ePubs).
But I must agree, I've never seen any regular publisher or commercial titles make use of it. Check out editions of Wilson's Life on Earth (Unit #1 is free).