This theory isn't citing the report itself, but independent analysis that's been done on the same data. The Wikipedia article on the topic has a whole section for these [1], and a section about this theory in particular [2].
Furthermore. The official accident report for crashes is not always considered the authoritative source for what happened. One good example is EgyptAir Flight 990 which the official report claims is a mechanical failure [3], but which is widely considered to have been pilot suicide. In that case the Egyptian investigative body was thought to be politically motivated.
Similarly, it's not at all implausible that the French BEA would be reluctant to make conclusions that could result in the grounding of the entire worldwide Airbus fleet while they're retrofitted with Boeing-style controls while France is the main Airbus manufacturing partner country.
1. https://en.wikipedia.org/wiki/Air_France_Flight_447#Independ...
2. https://en.wikipedia.org/wiki/Air_France_Flight_447#Sidestic...
3. https://en.wikipedia.org/wiki/EgyptAir_Flight_990