"Empirical" just means they discretized it.
The original Hull-White (1987) paper has $\alpha_{v,t} = \mu v_t$, but I'm not sure that is correct, because the log-variance doesn't have mean-reverting behavior.
If you let $Y_t = \log S_t$ (log price) and $h_t = \log( V_t)$ (log-volatility), $\alpha_{v,t} = (\theta - \alpha \log v_t)v_t$ ($\alpha > 0$), $\beta_{v,t} = \sigma v_t$ and apply Ito's lemma, you get
\begin{align*}
dY_t &= \left(\mu - \frac{v_t}{2}\right)dt + \sqrt{v_t} dB_{1t}\\
dh_t &= \left(\theta - \alpha\log v_t - \sigma^2/2\right)dt + \sigma dB_{2,t}\\
&= \alpha\left(\tilde{\mu} - h_t \right)dt + \sigma dB_{2t}.
\end{align*}
According to this, this was a model investigated by a guy named Wiggins. The log-variance follows an Ornstein-Uhlenbeck process, which is like a continuous time version of an AR(1). If you use the Euler-Maruyama method to discretize this, setting $\Delta t = 1$, you should see this
\begin{align*}
h_{t+1} &= \alpha \tilde{\mu} + h_t(1-\alpha) + \sigma \eta_t \\
&= \tilde{\mu}(1 - \phi) + \phi h_t + \sigma \eta_t \\
&= \tilde{\mu} + \phi(h_t - \tilde{\mu}) + \sigma \eta_t
\end{align*}
letting $\phi = 1-\alpha$. Note that $\tilde{\mu} \neq \mu$.
As far as the observation process goes:
\begin{align*}
y_{t+1} = Y_{t+1} - Y_t &= (\mu - \frac{v_t}{2}) + \sqrt{v_t}\epsilon_{t+1} \\
&= \left(\mu - \frac{\exp h_t}{2} \right) + \exp[ \log \sqrt{v_t}] \epsilon_{t+1} \\
&= \left(\mu - \frac{\exp h_t}{2}\right) + \exp\left[ \frac{h_t}{2}\right] \epsilon_{t+1}
\end{align*}
- I can't quite get the drift term to cancel out. The mean of these returns should be $0$. Maybe because that's because of some arbitrage argument I'm not privy to, or maybe it has to do with how the errors are correlated in the SDE.
NB: In the discrete time observation equation you wrote, you should set $\beta = 1$, otherwise the model isn't identifiable (because we have a non-zero mean for the log-variance process). This is mentioned in the paper you linked to, but it is also discussed on a thread on this site here.