1. To be an X of the gaps, you need to propose a specific cause for some phenomenon. If God = X, then it becomes "We don't know how this could happen, so God did it." But science isn't a cause, it's a methodology, so to say "Science did it" doesn't make sense, it doesn't fit the formula of a God/science/whatever of the gaps. we don't say, "We don't know how this could happen, so religion did it." That makes no sense, just like "science did it."
2. Even if you make X = nature, you don't need to assume that there is a natural cause in order to understand that science doesn't have all the answers (yet). Science, despite what others around here may say, is perfectly capable of investigating supernatural causes; there is a long history of scientific studies on ESP, telekinesis, and other supernatural phenomenon. Now, I think the entire distinction between natural and supernatural doesn't make any sense, but if you accept the distinction, there is no necessary nature of the gaps.
So, rather than asking another question, or continuing on about science of the gaps, why don't you lay out, in assertions that reference evidence in a logical fashion, why the failure to fully explain how organelles evolved refutes the theory of evolution. Or, you could assert that that failure doesn't refute evolution, I don't want to put words in your mouth.