1. assumes the validity of the scientific method
2. relies on the scientific method as its critical lens
Whereas those who critique science as a whole:
1. assume that the scientific method does not work and does not arrive at "truth"
2. then use scientists being self critical to prove #1.
Such a "proof" does not work as there is its uses the assumption "the scientific method arrives at truth" to derive the contradiction "the scientific method does not arrive at truth". See for instance comment: https://news.ycombinator.com/item?id=16859200
In reality, work on reproducibility is about improving the practice of science overall. It does not in itself show that science is inherently untrustworthy. What it does show is that scientific discovery is difficult and it takes a lot of effort and new findings should be treated critically. What does critically mean in this context? It means with in the boundaries of science analyzing the theoretical basis, hypothesis, method, and experimental results for potential flaws. It does not mean to be skeptical as a default because science "doesn't work."