That is true, and an important criticism of IQ as a measure in general. However, it's not clear that the Flynn effect is relevant to the conclusions of this study. Why do you think it is?
The study you linked was interesting but adopted kids are an abnormal case to begin with and the effect indicated was tiny compared to societal things IMO.
However, a ray of hope in the study is that, even if you take its confidence intervals at face value (I don't), then there is quite a bit of room for improvement in the nurture sphere, as the black/white IQ test gap is generally much larger than this when not as carefully controlled as this study.