Salmon story is more than a decade old at this point, and still as relevant as before; became an instant classic in my neuroscience-related MS programme. This Wired article elaborates on the motivation behind the study:
The takeaway from Salmon experiment IMO is not specific to fMRI: you cannot trust a single technique or field "golden" standard (whether flawed or not), and should rather pursue accuracy across different pre- post-processing methods.
That's not realistically doable single-handily (at least in my experience), but in the current age it should become the norm to rely on publically available pipelines, probably with some sort of configuration files or even GUIs. I personally worked with fMRI only sparingly, so cannot comment on that in the context of the posted article.