On the one hand, I appreciate that they're trying to put numbers on a problem we all feel in our gut. You can't hand-wave it away by saying "well, things change".
But, at the same time, things DO change. At a time when many goods and services are at an all-time low in terms of costs, why WOULDN'T housing costs go up? On the one hand, costs will be affected by constrained or increased supply. On the other hand, there's the demand side. If I can afford to cheaply feed and transport and clothe myself, why would I not choose to allocate a greater share of my income towards housing closer to work, or with more space, or in a more desirable neighborhood? The choices we all freely make with how to allocate our income necessarily drives affordability for others.