The substrate of an enzyme can be any one of a huge number of molecules indeed there are enzymes that convert L-amino acids into D-amino acids.
Yes, you are right on. these enzymes are known as racemase enzymes. They are not present in every cell.If they are present, then all reactions will proceed. There will not be any enzyme inhibition. But, in nature, this is not the case. Threre are specific control mechanisms modulating cellular activity. What happens if there is no control? This is when we develop some diseases known as Metabolic disorders. For example, if Phenyl alanine is not metabolized, then it accumulates. The clinical condition is known as Phenylketonuria.
Random chemical reactions cannot and should not occur. If they did, then there will be chaos and severe metabolic disorders.