not necessarily. Only if habitat is not protected and/or too much land is used to cultivate bioengineered species. If bioengineered species are commercially more successful one new species could substitute for a variety of previously grown cultivars. But one can say exactly the same about modern large-scale agriculture. 100 years ago many more cultured varieties were grown. It's the focus on organisms only with commerical value which damages biodiversity, not the process of biological engineering. You could also argue that the possibility of bioprospecting with the aim for later biological engineering encourages conservation of wild areas for their potential value in yet undiscovered genes with desirable properties.
Like any tool biological engineering can be used to benefit or damage biodiversity. It's the use it is put to which does the damage, not really the tool itself.
