Traveling Salesman -- number of qubits required?
The notebook describes how to solve combinatorial optimization problems by encoding them as minimizing a binary quadratic form, which can in turn be phrased as finding the minimal eigenvalue of a Hamiltonian, and so solved by a quantum computer. The number of qubits needed is the dimension of the Hamiltonian, which is also the number of bits in the encoding.

In TSP, the optimization is over permutations. The notebook suggests encoding a permutation by encoding its permutation matrix, which is an $n\times n$ binary matrix. Since the rows and columns sum to 1, we can deduce the final row and column from the rest of the entry, and so need to keep only $(n-1)^2$ variables. In your example, $n = 4$ and so $(n-1)^2 = 9$.