As the article says, I think that in general this is not the only problem in electrochemistry research. I think there is a lack of regulation in terms and procedures for electrochemistry by IUPAC or other institutions that set the scientific consensus. I suppose this has to do with the fact that the deepening of electrochemistry as a research branch is relatively modern compared to others. I have seen papers with very good results but with failures, I think that in part it has happened to all of us that we are learning many things as we advance in the path of electrochemistry, because there is still a lack of clarity in some aspects.
Forward: I read the linked article and the abstract of an underlying paper, but have not fully read any underlying papers.
I'm a bit confused because the underlying paper compares the reference electrodes with an RHE at different pH levels, but the RHE by definition has a potential which varies with pH so of course the measured potential with other reference electrodes will be different--this may be better explained in the full text, but without that, I'm, as I said, a bit confused.
A stable reference electrode potential is a stable reference electrode potential even if there are additional potential drops from electrolyte activity to be considered. If the environment is causing the reference potential to become unstable (e.g. by ingress through the frit) then that would be concerning. If researchers are comparing across different reference potentials, particularly to RHE (which is not a single potential value), without considering the effects of activity, that would also be an issue.
For a not insignificant fraction of electrochemical testing an ideal, formal reference electrode is not really workable, and so quasi-reference electrodes, internal electrochemical standards, and other "tricks" can be necessary. It is important to understand the limits of reference electrodes but it doesn't strike me as alarming to do electrochemistry with a non-ideal reference electrode, provided it is stable and they are documenting what they are using and the values the are getting from that.
The reference electrode is, fundamentally, there to ensure that all changes in measured voltage in a 3-electrode system, are only due to changes in the potential at the working electrode interface. It has the added benefit, in well controlled settings, of allowing other researchers to double check results. Using the same conditions should produce the same results.
If a given reference electrode is fundamentally unstable, and leads to erratic results, then it's a bad reference electrode. If researchers are using bad math to adjust potentials and then making claims about a catalyst, well, that's bad math, not a bad reference electrode.