I would also caution against your interpretation of the quote in bold; I think the quote is meant to reflect the author’s following statement from the NIST paper in JoGG rather than the sentiment you implied:

“A bigger problem for the genetic genealogy community is that different DNA test providers may have different nomenclatures for calling the same Y-STR allele. It is important for users of these DNA test results to appreciate that these differences arise in how a STR repeat sequence is denoted by the laboratory and not because of some measurement mistake.” J.M. Butler, M.C. Kline and A.E. Decker. Addressing Y-chromosome short tandem repeat (Y-STR) allele nomenclature. J. Genetic Genealogy 4:125-148 (2008).

Thus, the differences usually arise from HOW the company measures and reports the allele, not mistakes in measuring the allele.

And one can compare results from one company to another, as long as they take care to note that the companies might have reporting differences. The genetic genealogy community is well aware of these reporting differences, and is working with the NIST to make reporting more uniform. Additionally, there are sites available to convert reporting from one company to another company’s format (usually there are only a very few reporting differences).