There's been some discussion about the single CPET, and some persuasive arguments for just using the one CPET.
The thing is, as Todd Davenport says, the measures reduce from CPET to CPET in ME/CFS (and presumably also with other pre-test activity). If it's true that CPET measures that are relatively constant from test to test in healthy people vary a lot in people with ME/CFS, then a correlation between an outcome from only one test and an outcome from some other investigation such as muscle fibre composition won't necessarily be accurate. At least if you did two CPETs, you would know if trying to make such correlations was a fraught exercise.
I guess it's pointless wishing that the intramural study had been different, but, it could and should have been. There could have been three visits to spread the studies out, for example, if the NIH really wanted to do a good study, including 2 x CPET.
I do think that we need to understand what happens when people do repeated demanding activity, in terms of exercise physiology. I still think we need that study I've talked about before where people do three CPETs, each spaced a day apart, looking for reducing performance. If we can identify something that is markedly different between people with ME/CFS and healthy controls, then we have a clue.