Scale up operations encompass varied biotic and abiotic stressors like light quality, intensity, water quality and many more. The use of native species increases the probability of survival at scale up due to the species' innate ability to adapt. In the same scenario, if a foreign species is brought to a new environment, it may require adaptation studies prior to scale up operations. Furthermore, when looking at marine species, most coasts vary in their water quality (with respect to salinity, nutrient profile etc) and hence growing an indigenous species will be much less efforts on the growth engineering front.
While your argument for cultivation of non-native species to reduce contamination may be right in some context, I still believe it would not overcome the problem of pond crashes completely. When I say a native species is preferred for scale up operations, I mean a "robust and adapted" species. If inoculated in sufficient density, the organism will be able to overcome any foreign growth. Having said this, the cultivation of native species is also economically more feasible for any set up. Pond crashes are a problem everyone in the industry is combating and whether a native species is used or not, crashes can't be circumvented completely.
Open ponds are vulnerable to contamination. This
risk can be minimised by altering culture conditions,
making them unfavourable to native species.
This implies that cultivation media can be made unfavorable to native "grazers and unwanted species" and doesn't necessarily imply adoption of non-native species.