Both models are based on a spread, which has to be as stationary / mean reverting as possible.
$ y_t = \beta_0 + \beta_1 x_t + \epsilon_t $
In pairs trading, $y_t$ and $x_t$ are log prices, and (e.g.) the Johansen cointegration test is used to identify candidates for a pairs trade. For entry and exit points an error correction model is used. In the Avellaneda & Lee (AL) paper the $y_t$ and $x_t$ are indeed the returns. Mean reversion is modeled as an Ornstein-Uhlenbeck process on the cumulated residuals
$ X_k = \sum_{t=1}^k \epsilon_t,\ \ k = 1,2,...,T$
which are stationary (mean zero) by construction. Since the residuals are cumulated or 'integrated' they are stable and may display mean reversion, much like in traditional pairs trading.
I see two important differences: the AL method is (as the title says) a statistical arbitrage approach where $x_t$ are risk factors or baskets of securities, such as the PCA and ETF examples in the paper: it is not limited to pairs. Also, in AL there is no explicit test of the cointegration strength, as the mean reversion is built into the model.