"Twice two makes four" means, in the book, the truth that is not up for debate: the necessity of the laws of nature and of mathematics, against which the underground man rebels. He sees it first as a wall and then as the beginning of death.
In Chapter III, the narrator lists the truths before which men of strong nerves calm down: the laws of nature, the conclusions of the sciences, mathematics. If they demonstrate to him that he descends from the monkey, he must accept it. All of them bear the same seal: "because twice two is mathematics. Just try to argue with it."
In Chapter IX, the formula becomes a goal: man perhaps loves the process of arriving, and not the arrival. "And twice two makes four is no longer life, gentlemen, but the beginning of death." A ready-made formula is the end of the search, and without searching he sees nothing left to do.
Hence the concession in a jesting tone: "I agree that twice two makes four is an excellent thing; but if we are to praise everything, then twice two makes five is also, at times, a charming little thing." The five is not a thesis of arithmetic, it is a gesture of caprice. In the last chapter of Part One, he himself admits knowing, as he knows that twice two makes four, that the best thing is not the underground.