I seems like it's only part of the story. If you increase exercise but also increase calorific input to match then you won't lose weight. But, the laws of energy conservation being what they are, I don't think anyone disputes that if you very significantly increase exercise but also maintain calorific input then you will lose weight as the energy must come from somewhere and there are only so many optimisations your body can make. You could of course maintain exercise levels and reduce calorific input for a similar effect, ignoring health benefits of exercise. Take an extreme case, Michael Phelps. He used to eat 12,000 cal a day because of the hours he spent swimming. Certainly not a small guy but pretty lean! So I'm totally prepared to accept there are bounds to all these statements but I still think I couldn't finish an 800 cal sandwich for lunch hehehe.
By the way, I feel the Wikipedia page there uses a lot of words suggesting that the paradox isn't at all fully understood and that there could be compensating mechanisms we aren't aware of. But I'm not in a position to dig deeper.