Well, without being a coder I understand that epub is basically a html5 file and that some features of ePub consider page orientation. So it should be possible to take into account the alternate layouts of Indesign and add some coding or some export tagging.
As to the folio builder; why was this feature discontinued ? I came across this only after extensive reading through lots of help menus as Adobe help still gives advice on this CS6 feature and some tutorials still exist on youtube.