In concrete terms, a
reference point or
point of reference is a fixed point which can be used to refer to other points. When you say, "the third item from the end," the item at the end is being used as the point of reference.
In figurative or literary terms, the meaning is more nebulous. I was a little confused by it as well. It's important to realize that all English writing is not equally clear; some writers intentionally write in a way that clouds the real meaning (sometimes called "obfuscation") for various reasons. I think you are seeing some of that in your quoted passage, though it doesn't help that its original context is mostly missing.
Having said that, it's true that if there is a large area of knowledge about which someone knows very little, it is difficult to try to think about or describe a single concept within that area. That's because when we explain concepts, we do so with reference to other more basic concepts. If he or she can understand at least one concept within that larger area of ignorance, it becomes possible to examine other concepts by asking how they are similar to or different from the one that's understood. In this situation, the understood concept becomes like a point of reference from which attempts to grasp the others can be made.