It doesn't matter whether you formulate the Dickey-Fuller regression with $y_t$ or $\Delta y_t$ on the left hand side.
The $t$-statistics are exactly the same.
It's a matter of preference.
(The second formulation seems more common.)
First Regression
The Dickey-Fuller regression
$$
y_t = \gamma y_{t-1} + \epsilon_t,
$$
is not robust with respect to serial correlation in the error term $\{ \epsilon_t \}$.
The augmentation of the regression by lagged terms comes from an attempt to control for such serial correlation---specifically, in the case where the error term follows an ARMA process.
Suppose $\epsilon_t$ follows an ARMA(1,1) specification:
$$
y_t = \gamma y_{t-1} + \epsilon_t,
$$
where
$$
(1 - \phi L) \epsilon_t = (1 - \theta L) \nu_t.
$$
$L$ is the lag operator and $\{ \nu_t\}$ is white noise.
The inverted MA representation of $\epsilon_t$
$$
\nu_t = (1 - \theta L)^{-1} (1 - \phi L) \epsilon_t = \sum_{h = 0} \psi_h \epsilon_{t-h}
$$
implies
$$
\epsilon_t = \psi_1 \epsilon_{t-1} + \psi_2 \epsilon_{t-2} + \cdots + \nu_t.
$$
Substituting back into the model,
$$
y_t = \gamma y_{t-1} + \psi_1 \epsilon_{t-1} + \psi_2 \epsilon_{t-2} + \cdots + \nu_t.
$$
Under the unit root null $H_0: \gamma = 1$, $\epsilon_t = \Delta y_t$. So the regression model becomes (with linear trend)
$$
y_t = \alpha + \beta t + \gamma_1 y_{t-1} + \psi_1 \Delta y_{t-1} + \psi_2 \Delta y_{t-2} + \cdots + \nu_t.
$$
The Dickey-Fuller statistic is the $t$ statistic for testing $H_0: \gamma_1 = 1$.
Second Regression
Subtracting $y_{t-1}$ from both sides,
$$
\Delta y_t = \alpha + \beta t + \gamma_2 y_{t-1} + \psi_1 \Delta y_{t-1} + \psi_2 \Delta y_{t-2} + \cdots + \nu_t.
$$
The Dickey-Fuller statistic is the $t$ statistic for testing $H_0: \gamma_2 = 0$.
Simple regression algebra tells you that $\hat{\gamma}_2 = \hat{\gamma}_1 -1$.
Moreover the standard errors are the same---these two regressions have the same residuals and regressors. This implies the standard errors of $\hat{\gamma}_2$ and $\hat{\gamma}_1$ are the same. So the $t$-statistics are the same.