I read the original article, and Wang et al. measure fitness by (i) measuring photosynthesis in glasshouse-grown plants (ii) measuring seed germination on wet paper in petri dishes and (iii) growing plants in garden (grown 20 cm apart, fertilized, hand-weeding and insecticides applied).
We probably can assume that the extra copies of EPSP synthase genes increase the metabolic throughput (by boosting some of the protein synthesis pathways) of the plants, and when grown in abundant light (20 cm apart, no shadowing and competition from neighbouring plants), water and nitrogen (grown in garden conditions, fertilized), it is plausible that these individual grow faster and larger. This is all that Wang et al. did and all that their article claims.
The higher throughput capacity only comes into use if supplies of energy or raw materials are not bottlenecks.
But the Nature News conclusions "effects of such modification have the potential to extend beyond farms and into the wild" and "genetic diversity [of wild rice], which is really important to conserve, could be threatened because the genotype with the transgene would outcompete the normal species" are very much unsupported by the results of Wang et al.
In the wild, seeds may need to germinate in more challenging conditions that wet paper on a petri dish, there may not be abundant light, nitrogen or water.
So the EPSP synthase -boosted plants grow better in the garden. But maybe there is a good reason why the EPSP synthase levels are lower in the plants from the wild. Maybe something else is more valuable to them, something that helps in e.g. low-light photosynthesis, nutrient or water uptake in scarce conditions, or defence against insects. Maybe the wild EPSP levels are just optimal for growing in wild conditions and the plants with boosted EPSP synthase levels would have lower fitness in wild conditions. (I assume that the higher levels of the synthase don't come for free, but have a related metabolic cost that cannot then be used elsewhere).
As Wang et al. only measured fitness in garden, not in the wild, the Nature News conclusions are unwarranted.