As all engineering, it boils down to requirements. Mycoplasmata, from which JCVI-syn3A has been developed, is reported to "survive without oxygen", which means

As all engineering, it boils down to requirements. Mycoplasmata, from which JCVI-syn3A has been developed, is reported to "survive without oxygen", which means that it's not necessarily a "pure" anaerobic organism. We must assume that there has to be an existing mechanism that protects this bacteria from highly reactive oxygen. If the design requirements don't include surviving the natural environment, then that is one of probably many more areas to trim genetic "fat" from. However, I don't know much about their work on synthetic bacteria nor the environment used for it, so it's possible that the aforementioned mechanism to be already removed from its genes.