Why don't things work with comparisons in reference letters and refereeing?
I suggest that an academic committee, sitting in consideration of an applicant to their PhD programme, would very likely view your addendum as being an honest attempt to preserve your set of professional ethics with regard to fairly ranking the applicant.

I do not think that the academic committee would doubt your trustworthiness. However, I expect that the committee would view whatever ranking you provided on the Good/Great/Excellent/Outstanding/Genius scale in light of your action of submitting your addendum. 

Therefore the committee are not going to doubt your ability to rank the applicant, but are going to doubt the veracity of your ranking on the artificial scale. 

However, I would hope that any sensible academic committee is going to be aware of the problem that we are discussing here and are therefore going to take a scaled single-valued ranking of any applicant with a massive grain of salt. They must know that a single value rank is going to be useless when judging the suitability of an applicant for a PhD programme.

Thus I would hope that, with or without your addendum, a sensible academic committee would take very little notice of the single value ranking and pay much more attention to the substantive letters of recommendation.

The addition of your addendum would not, I think, damage the applicant's application before a reasonable academic committee, as it wouldn't be news to the committee that such single-valued rankings are untrustworthy. To a reasonable academic committee, your actions of submitting the addendum might prompt others to do the same, and the practice of demanding a single-value metric abandoned over time. To an academic committee that places great store in such single-value metrics, your addendum sets out your concerns and presumably instructs the committee how you the single-value ranking is to be interpreted.