This is a bit complicated. You have misunderstood the authors' intent. Meanwhile, the authors have overlooked the fact that $W$ is symmetric. Although one can simply consider $W-\frac1n\mathbf1\mathbf1^T$, the authors had opted to consider $(W-\frac1n\mathbf1\mathbf1^T)(W-\frac1n\mathbf1\mathbf1^T)^\top$ unnecessarily.
First, you wrote
In the footnote, it claims that the eigenvalues of $(W-\frac{1}{n} {\bf 1} {\bf 1}^\top)$ are less than 1 since the eigenvalues of $(W W^\top - \frac{1}{n} {\bf 1}{\bf 1}^\top)=(W-\frac{1}{n} {\bf 1} {\bf 1}^\top)(W-\frac{1}{n} {\bf 1} {\bf 1}^\top)^\top$ are less than 1.
That wasn't what the authors meant. What they wanted to prove is not that the eigenvalues of $A=W-\frac{1}{n}\mathbf1\mathbf1^\top$ are less than $1$ in size, but that the spectral norm of $A$ is less than $1$. In other words, they wanted to prove that the eigenvalues of $AA^\top$ are strictly less than $1$.
However, by definition (see sec. II A on p.3), the doubly stochastic matrix $W\in\mathbb R^{n\times n}$ in the paper is a weight matrix of an undirected connected graph $E$ such that $w_{ii}>0$ for each $i$. Hence it is necessarily symmetric and irreducible. The eigenvalues of $AA^\top$ are just the squares of the eigenvalues of $A$. So, it does suffice to prove that the eigenvalues of $A$ are less than $1$ in sizes. Although you have misunderstood the authors' intent, your (mis)interpretation of their strategy also works.
At any rate, since $W$ is a symmetric irreducible doubly stochastic matrix with a positive diagonal, so is $WW^\top$. (In general, $WW^T$ is not necessarily irreducible, even if $W$ is primitive, but in our case, $W$ is an irreducible matrix with a positive diagonal. Therefore $WW^T$ is primitive and hence irreducible.) We want to show that all eigenvalues of $S-\frac1n\mathbf1\mathbf1^\top$ are less than $1$ in sizes when $S=WW^\top$ (the authors' intent) or when $S=W$ (your interpretation).
Since $S$ is irreducible and doubly stochastic, by Perron-Frobenius theorem, $1$ is a simple eigenvalue of $S$ and the moduli of all other eigenvalues of $S$ are strictly less than $1$. Thus we can arrange the eigenvalues of $S$ as $\lambda_1(\,=1)>\lambda_2\ge\cdots\ge\lambda_n\,(>-1)$. Since $S$ is also symmetric, we can pick an orthogonal eigenbasis $\{v_1=\mathbf1,v_2,\ldots,v_n\}$ with $Sv_i=\lambda_iv_i$. Then $\mathbf1^\top v_j=v_i^\top v_j=0$ when $j\ge2$ and
\begin{cases}
(S-\frac1n\mathbf1\mathbf1^\top)v_1=S\mathbf1-\mathbf1=0,\\
(S-\frac1n\mathbf1\mathbf1^\top)v_j=Sv_j=\lambda_jv_j\text{ when } j\ge2.
\end{cases}
Hence the eigenvalues of $S-\frac1n\mathbf1\mathbf1^\top$ are $0,\lambda_2,\ldots,\lambda_n$, which are strictly less than $1$ in moduli.