Note that your statement
$\hat{u}_{t}$ is uncorrelated with $X_{t}$ by properties of OLS residuals.
is sample-dependent, in the sense that OLS normal equation only says $\sum_{t=1}^{T}X_{t}\hat{u}_{t}=0$, meaning the full statement should be
$\{\hat{u}_{t}\}_{t=1}^{T}$ is uncorrelated with $\{X_{t}\}_{t=1}^{T}$ by properties of OLS residuals.
But what is the value $\sum_{t=2}^{T}X_{t}\hat{u}_{t}$ or $\sum_{t=3}^{T}X_{t}\hat{u}_{t}$? I have no idea. As a result, will $\{\hat{u}_{t}\}_{t=2}^{T}$ and $\{X_{t}\}_{t=2}^{T}$, $\{\hat{u}_{t}\}_{t=3}^{T}$ and $\{X_{t}\}_{t=3}^{T}$ still be uncorrelated? I don't think so.
Now go back to your question.
The general auxiliary regression for testing up to $p$-th order auto correlation is
$$\hat{u}_{t}=\gamma^{\top}X_{t}+\sum_{j=1}^{p}\alpha_{j}\hat{u}_{t-j}+\varepsilon_{t}.$$
Since you include the lag terms of $\hat{u}_{t}$, which forces the sample indices of above regression equation to be $t=p+1,p+2,\ldots,T$. As mentioned before, generally, this will cause the regression result of $\gamma$ deviating from 0. (Although under null $\mathbb{E}[u_{t}|X_{t},u_{t-1},\ldots,u_{t-p}]=0$, these coefficients should converge to 0, but that's exactly what we are testing here.)
You can also verify it by a simple numerical experiment. Run a simple OLS regression, then i) regress $\hat{u}_{i}$ on $X_{i}$ using all the samples, you will get 0. ii) do the same regression but delete the first sample $\hat{u}_{1}$ and $X_{1}$, the result is no longer 0.
Updates.
To cut a long story short, in the auxiliary regression, omitting $X_{t}$ won't cause inconsistency, but will contaminate the asymptotical distribution, hence the inference.
If we use $u_{t}$ in the regressor, then your claim is true, omitting $X_{t}$ is totally fine. However, the situation becomes different when we replace $u_{t}$ by $\hat{u}_{t}$.
Denote the original regression as
$$y_{t}=\beta^{\top}X_{t}+u_{t},$$
under contemporaneous exogeneity, the infeasible auxiliary regression is
$$u_{t}=\tilde{\delta} u_{t-1}+\tilde{\varepsilon}_{t}. $$
Since $u_{t}$ is not observable, we replace them by $\hat{u}_{t}$. Note that $\hat{u}_{t}=u_{t}-(\hat{\beta}-\beta)^{\top}X_{t}$, therefore despite the true parameter before $X_{t}$ was exactly 0, now it becomes weird
$$\hat{u}_{t}=-(\hat{\beta}-\beta)^{\top}X_{t}+\delta\hat{u}_{t-1}+\varepsilon_{t}.$$
This equation is kind of beyond traditional econometric setting since the pseudo-true value $(\hat{\beta}-\beta)$ itself is changing and converging to 0. For now, let's first take sample size as fixed.
By direct computation, if $X_{t}$ is omitted in above regression, we have $\hat{\delta}=\delta-A_{T}+(\sum_{t=2}^{T}\hat{u}_{t-1}^{2})^{-1}\sum_{t=2}^{T}\hat{u}_{t-1}\varepsilon_{t}$, where the bias term of $\hat{\delta}$ is
$$A_{T}=\biggl(\frac{1}{T}\sum_{t=2}^{T}\hat{u}_{t-1}^{2}\biggr)^{-1}\frac{1}{T}\sum_{t=2}^{T}\hat{u}_{t-1}X_{t}^{\top}(\hat{\beta}-\beta).$$
Now let's see what happens when $T\to\infty$, follow some standard procedure, we have
$$\begin{align*}
\frac{1}{T}\sum_{t=2}^{T}\hat{u}_{t-1}^{2}&=\mathbb{E}[u_{t}^{2}]+o_{p}(1)\\
\frac{1}{T}\sum_{t=2}^{T}\hat{u}_{t-1}X_{t}^{\top}&=\mathbb{E}[u_{t-1}X_{t}^{\top}]+o_{p}(1)\\
\sqrt{T}(\hat{\beta}-\beta)&\overset{\mathcal{L}}{\to}Z_{1}.
\end{align*}$$
Combine above result, the bias term*
$$A_{T}=O_{p}(1)O_{p}(1)O_{p}(T^{-1/2})=\color{red}{O_{p}(T^{-1/2})},$$
which indicates $\hat{\delta}$ is still consistent. The problem arises when we apply the traditional $t$-test for $\delta$, CLT gives
$$\sqrt{T}(\hat{\delta}-\delta+A_{T})\overset{\mathcal{L}}{\to}Z_{2}.$$
Here $Z_{2}$ is the normal distribution that $t$-test based on. However, when normalized by $\sqrt{T}$, the bias term $A_{T}$ will show up in the limiting distribution of $\sqrt{T}(\hat{\delta}-\delta)$ since $\sqrt{T}A_{T}=O_{p}(1)$, hence the $t$-test no longer works.
*: If you strengthen contemporaneous exogeneity $\mathbb{E}[u_{t}|X_{t}]$ to strict exogeneity $\mathbb{E}[u_{t}|X_{1},\ldots,X_{T}]=0$, that $X_{t}$ is not allowed to be correlated with past innovation, then $A_{T}=o_{p}(T^{-1/2})$ since the second term becomes $o_{p}(1)$, and $t$-test is still valid. This is what the textbook says.