One important difference is that recoded bacterial strains, while immune to phage, experience a very wide range of fitness defects due to breaking of adaptive epistatic interactions by the recoding. These defects are very significant even in controlled lab environments, with recoded strains growing very slowly. In heterogenous environments these problems are even more severe. Mirror bacteria would not experience these defects as all genetic interactions would be preserved (although, without further engineering, they would not have an optimal nutrient acquisition profile).
I agree that this kind of work deserves scrutiny, however.
I think you linked to the wrong article?
One important difference is that recoded bacterial strains, while immune to phage, experience a very wide range of fitness defects due to breaking of adaptive epistatic interactions by the recoding. These defects are very significant even in controlled lab environments, with recoded strains growing very slowly. In heterogenous environments these problems are even more severe. Mirror bacteria would not experience these defects as all genetic interactions would be preserved (although, without further engineering, they would not have an optimal nutrient acquisition profile).
I agree that this kind of work deserves scrutiny, however.