I want to design an alien species whose physiology is capable of metabolizing substances regardless of whether their chemical chirality is levorotatory or dextrorotatory. Is this scientifically possible, and if so, what would be required?
Its not going to be a problem. Humans and animals already have some ability to digest D-isomers of amino acids (though results significantly vary from one amino acid to another). In a world where D-isomeres are widely available, it's logical to assume that animals would have the necessary enzymes to process not some, but all D-isomers.
This is all assuming that the species of this world, like here on Earth, would have a strong preference for one type of enantiomers. So, some species would like D-isomers, some L-isomers, and they can be a viable food source for each other.