I wouldn't say "called into question", as if the whole idea is bunk.

MRI is, in general, a lot harder than people often imagine. It uses complicated physics to measure convoluted physiological changes to indirectly measure brain activity, which is obviously stupifying involved--and then relate that to other, often complicated factors like behavior, lifestyle or disease state.

I think it's reasonably well-known that the BOLD response is complex and doesn't directly reflect "average" spiking activity. Some studies find that it's sensitive to the amount of synchrony (=more neurons firing together in time) rather than the rate. The paper you mention shows another dissociation: neurons can get more fuel by extracting oxygen more efficiently OR have having more overall oxygen to extract at the same rate. Thus, it's not noise, but it is complicated.