I believe WADA will certify the test, and several other labs did testify, during the hearing, that they would interpret that same data as a positive.
In theory the actual tests, and therefore the standards, are determined by peer review and scientific studies. WADA will then say "yes, this test is reliable" or "no, it's not good enough."
Some of these tests are highly interpretive. I may be wrong, but the isotope test isn't too interpretive though -- either you have the isotopes associated with synthetic testosterone in your blood, or you don't. Isotope signatures are fairly unique.
My recollection is that one or two of Landis' defense witnesses suggested the technicians did not operate the machine properly. I don't remember anyone saying that the standards themselves were moving targets.