HEAVY SPOILERS AHEAD.
This anime is rife with Gnostic symbolism and themes. The meaning of Re-l's name is actually very critical to understanding the point of the entire show. Before I can tell you the meaning of Re-l's name, you need to understand a bit about the Gnostic themes expressed in Ergo Proxy.
The main thing you need to know about Gnosticism to understand the meaning behind the names Re-l and Real is that Gnostics endeavor to achieve union with God, where a human can truly touch the Divine.
This steps beyond the dogmatism of monotheistic religious beliefs. What Gnostics seek is a realization of "true reality." For the Gnostics, who were very much influenced by Neoplatonism and Plato's idea that this true reality exists beyond the physical, material world. In this physical world, we are condemned to suffering and repetition of all our mistakes. Plato believed true Reality exists in the Mind. For Plato, that which is real is an idea. This most well-known articulation of this conception of our place in the world is expressed through Plato's famous allegory of The Cave. To some extent, we can think of the life of illusion that "everything is okay" experienced by the "fellow citizens" in the dome cities is a parallel to the people tied up in Plato's Cave. When Re-l and Vincent begin their journey outside of the dome, they soon begin to see things as they really are, thus serving as a parallel for the person who escaped their bonds and ventures outside the cave. When Re-l and Vincent encounter the deformed, sluggish and sickly people in an actual cave filled with noxious poison gas, Re-l reflects on her experience in the Romdo. She notes that these people, in their effort to hide from the real world of suffering and pain, have stunted their development as beings. She realizes that they are not so different from the people in Romdo. This further serves to solidify that this theme in Ergo Proxy refers to Plato's Cave.
The Gnostics take this idea one step further by claiming that dogmatic religion up to this point has lied to us and kept us apart from the true Reality. Ergo Proxy does a good job of representing this lie told to us by society with the way the government of Romdo lies to its people, claiming it is for their own good. Plato believes we can find truth in the world outside the cave, while the Gnostics seek to become one with this truth. Ultimately, the meaning of the Gnostic ideal of union with God is something that has been interpreted in different ways by many different scholars. I have my own opinion about what this union with God looks like, but I am not going to go into that here. Here I am just going to answer the question, "What is the meaning behind Re-l's name?"
What Ergo Proxy offers us is an interpretation of the Gnostic ideal of union with God and the true Reality. Through their quest for knowledge, Re-l and Vincent learn about how the Proxies created the Domes so that people could continue their lives on this apocalyptic husk of a planet. At this point we learn the Real, an apparent clone of Re-l, is actually a reincarnation of Monad Proxy. Real urges Vincent to fly to the sky with her and abandon the world of suffering and pain below. However, Daedalus tells us that when Proxies are exposed to the sun, they die. The blue sky and sun above the clouds represents the true Gnostic Reality, and this interpretation is further supported by Plato's use of Light as a symbol for the Mind and the truth of ideas. The world of Earth, below the clouds, is dark and full of pain and suffering, but it is also the place where Vincent, as a Proxy, can live as a physical being with desires, pleasure, pain, and everything else entailed by living here. What this reveals is that Ergo Proxy is presenting the Gnostic Reality as bliss, complete unity with all of creation, and thus, oblivion. Yes--freedom from the physical form means relinquishing this physical form. To become part of the infinite is to relinquish the finite, and thus relinquish mortality, and indeed, life. To unite with God is to die, but also to stop suffering. We see this when Real flies to the clouds and disintegrates as a blur, merging with the greater cosmos.
Vincent, as a Proxy, occupies a space between this physical reality and the true Reality. Perhaps he is like the man who ventures outside of the cave in Plato's allegory. But Vincent was very much attached to the world of humanity, the imperfect, painful, dark and desolate world, but also the world full of beauty, innocence, and freedom to choose who you are among the finite. But what I do know is that at the very end, Vincent faced a choice, and this is ultimately where we come to the meaning behind the names Re-l and Real.
Real, the Proxy, offers Vincent a choice to join with the true Reality, if he would only fly up with her into oblivion. Re-l, the human, offers Vincent a choice to stay with humanity and be one of the mortals. They are indeed clones of each other, and their names are so close together yet significantly different. "Re-l" is fragmented, it is almost the full name "Real" but it is missing a letter--it an incomplete name--just like the incomplete physical reality that she represents. "Real" is the full name and she represents this true Reality, the implications of which I have discussed above. Real cannot stay in the physical world because she is destined to fly to the sky and become one with God, a realization which, in Ergo Proxy's interpretation, is oblivion.
At the end, Vincent made his choice. He chose the imperfect Re-l because he loved her. He chose this imperfect reality because he loved it. He abandoned his chance at unity with Reality because he saw this world as a world worth living in. He could never abandon this world.
This is just my interpretation of the meaning behind the names "Re-l" and "Real". Perhaps my interpretation is not what the creators of Ergo Proxy had in mind, but it makes sense to me. I also know there are so many other details and philosophical concepts explored in this anime, that I did not visit in this response. Really this is just my effort to answer the one question at the top of this page.