You're possibly conflating forward inference with backward inference. This is an important consideration, especially in brain imaging. It has been explicitly research and published about:
http://www.sciencedirect.com/science/article/pii/S1364661305003360
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240863/
In general, anytime you have a conditional, you shouldn't automatically assume the converse of the conditional is true, forward/reverse inference is the statistical analog of this. A simple example is that when you kick a ball, it's likely the ball moves, but every time the ball moves doesn't imply that it's equally likely it was kicked.
Specifically, I agree that A --> B (the study implies, through brain states, that subjective states are reliable) but they very explicitly mention that B -/-> A (subjective state reports do not imply a particular brain state). And this is exactly what degeneracy is. Degeneracy is an accepted fact of biological systems in general, and is especially applicable to the problem of forward vs. reverse inference in brain imaging.
I'll narrow down the previous quote for you so you can see where respect to the above is paid in the paper:
"Thus, generalizations between different pain states may be misleading. Pain is defined by the first-person experiential perspective and must be diagnosed and treated with significant consideration of the subjective report.
Thus, even if unique patterns of brain activity have been characterized in large numbers of patients for a given chronic pain state, the subjective report will likely remain the single most reliable index of the magnitude of pain."
(other than that the whole tone of the paper is that subjective reports are more reliable than brain imaging when you read it in full)
More on degeneracy in general in biological systems:
http://www.pnas.org/content/96/6/3257.short
http://www.pnas.org/content/98/24/13763.short
if you want to play with forward inference vs. backward inference, here's a meta-analysis tool for imaging studies. In imaging, you don't trust just one study in the first place, statistical confidence is generally weak, and that is the motivation behind this tool, but you also get to explicitly see how direction of inference affects the answer to your questions:
http://neurosynth.org/explore
You can read their FAQ about the specific difference of their particular instance of forward vs. reverse inference (and even posterior) here too:
http://old.neurosynth.org/faqs#faq8
It's not the general case of forward/reverse inference, but it's related.