Well, I only hope there will be a way to disable it. In the PDF file. Yes, I mean that I, as a PDF producer, decide what you, as a reader will see.
I think of it this way: Film used to be a 'fixed' presentation, even those with a break somewhere in the middle: that was what the director and editor designed it for. Today, with TV and commercial breaks, it is chopped up into a format that makes the film look bad -- and I think there has been at least one successful lawsuit (by a film directory against a TV channel) against this practice.
Some books are designed in a similar way, especially in PDF. The producer may spend an inordinate amount of time to get end-of-line hyphenations right, much as a film editor will do his utmost to get the timing of cuts right. The book producer will certainly not approve of a reflow introducing new hyphenation-by-algorithm errors. Same thing with avoiding orphans and widows. That is, the producer adds quality that reflow cannot maintain.
Of course, to some readers this doesn't make sense: they do not perceive any quality improvement. That doesn't matter: these readers will go for other versions of the book. But it would be unfortunate if their capability of recognizing quality was taken as the only true guiding star.