If you create a fxl ePub, you can use the same document for print and digital version. You might play with layers for some cases but it is possible. If you need to create a reflowable ePub, it would be hardly possible to retain the same file.
You can take a look to: Dropbox - FanfanLaTulipe_Print-Num_02.epub
It's a FXL epub sample exported from InDesign CC 2014.1.
IMHO, for economical reasons, the two versions (Print & digital) must have been designed in the same time.
That means the digital version can be finalized several minutes after the final print version and done for free because, when the print version is designed, we know we'll need a digital version.
as you created already an ePub and a PDF from the same InDesign File, you might have answered the question already yourself.
Or did you ask if the file could be printed to paper if only an fxl ePub exists? In this case, I think that no (or only under different conditions).
(EDIT: My previous post is missing: You can have the same InDesign-Document for print and fxl export. Creating a printable fxl ePub is theoretically possible, albeit with additional work. However, a practical case is not known to me.)
You might specify a set of CSS rules for print:
<link href="printme.css" type="text/css" media="print" />
It's a very common procedure for 'normal' HTML, so it might work all right... As long as you include this declaration in the head of all HTML files and you cover all the needed possibilities in the file printme.css so that no HTML class or id goes under the radar and breaks the printing. Anyway, that would be easily detected if you print to a PDF and then revise it.
Just an idea.
Gustavo (Posting from madrid)