Simply speaking - They chunk the document (make it smaller so that it can be sent to gpt) and then vectorize it (change it to numbers / vector array). From there that is stored in a vector store - now, when you query you first query your vector store for the context (part of the 50MB file) and then send the context along with the question to GPT.
You are right GPT-4 doesn't support fine-tuning but, I think (in general) people might be misunderstanding what fine-tuning does.