Isomers do tend to act differently in certain situations. You can't shake someone's left hand easily with your right. Although I'm not certain on the exact mechanisms I believe it is possible to screen molecules of different chiralitites by using chemicals that only attach to a right hand or a left hand partner. They might also pass through mazes and filters in different directions.

It's a good question, and I'd love to hear a detailed answer.

Yes, there are many ways to make isomers--it is done commonly in the pharmaceutical industry. Can be done directly via synthesis, or a racemic mix can be separated by physical processes such as crystalization or enzymatically. Most enzymes have a chirality (like the glove analogy), so they tend to create produces with a single isomer.

This said, making an organism with mixed chirality would likely not be effective because, likely, many reactions would not proceed or would proceed with poor efficiency. All D- or all L- would work fine, but any evolved organism would suffer/die with a mix of D- and L-.

There are ways of separating individual enantiomers from a racemic mixture of both. For example, crystallization will create separate crystals of each (this is how it was done first by Pasteur).