The point of instrumental variable regression is to provide an unbiased estimate of the causal effect of exposure $X$ on outcome $O$, when there is some unmeasured—possibly unmeasureable—variable $U$ confounding the relationship between $X$ and $O$. Here's a DAG of the simplest circumstance under which one would use instrumental variables estimation ($X$, $U$, and $Z$ can be sets of variables):
If an instrumental variable $Z$ causes $X$, has no effect on $O$ other than through $X$, there is no prior cause of both $Z$ and $O$, and the effect of $X$ on $O$ is homogeneous, then with a large enough sample $E[O|\hat{X}]$ where $\hat{X} = E[X|Z]$ can provide an unbiased estimate of the causal effect of $X$ on $O$.
In summary you do not care about the effect of $Z$ on $O$ (there is none except through $X$), and $E[O|\hat{X}] \ne E[O|X,Z]$, so simply including $Z$ in your model will not get you an instrumental variable estimate.
Final comment: The "...in the initial estimation?" closing of your question makes me want to clarify: one first estimates $\hat{X}$ (so $Z$ is indeed part of that estimation), and one uses $\hat{X}$ as a predictor in the second estimation (sans $Z$).