This is definitely a point of concern. Consistent testing methodology is necessary if you are going to compare results. However, I still have questions...
You say 28 is fewer cycles than most places use today. How do you know this?
How many more positive test results do you get if, for example, using 30 cycles instead of 28? How many more false positives? Are the differences really large or insignificant? What does the curve look like?
Intuition tells me that there is some number of cycles that gets you a desired high level of accuracy and going beyond that doesn't do much except perhaps to make recovered cases somewhat more detectable. After all, no number of cycles should tell you that you have are or have been infected with something you haven't. However, I don't confuse my intuition with actual science.