Proof.
Part (1) is the special case of part (2) where $U = X$. Choose a surjective étale morphism $U' \to U$ where $U'$ is a scheme. It is clear that we may replace $U$ by $U'$ and hence we may assume $U$ is a scheme. Since $X$ is quasi-compact, there exist finitely many affine opens $U_ i \subset U$ such that $U' = \coprod U_ i \to X$ is surjective. After replacing $U$ by $U'$ again, we see that we may assume $U$ is affine. Since $X$ is quasi-separated, hence reasonable, there exists an integer $d$ bounding the degree of the geometric fibres of $U \to X$ (see Lemma 68.5.1). We will prove the lemma by induction on $d$ for all quasi-compact and separated schemes $U$ mapping surjective and étale onto $X$. If $d = 1$, then $U = X$ and the result holds with $Y = U$. Assume $d > 1$.
We apply Morphisms of Spaces, Lemma 67.52.2 and we obtain a factorization
\[ \xymatrix{ U \ar[rr]_ j \ar[rd] & & Y \ar[ld]^\pi \\ & X } \]
with $\pi $ integral and $j$ a quasi-compact open immersion. We may and do assume that $j(U)$ is scheme theoretically dense in $Y$. Then $U \times _ X Y$ is a quasi-compact, separated scheme (being finite over $U$) and we have
\[ U \times _ X Y = U \amalg W \]
Here the first summand is the image of $U \to U \times _ X Y$ (which is closed by Morphisms of Spaces, Lemma 67.4.6 and open because it is étale as a morphism between algebraic spaces étale over $Y$) and the second summand is the (open and closed) complement. The image $V \subset Y$ of $W$ is an open subspace containing $Y \setminus U$.
The étale morphism $W \to Y$ has geometric fibres of cardinality $< d$. Namely, this is clear for geometric points of $U \subset Y$ by inspection. Since $|U| \subset |Y|$ is dense, it holds for all geometric points of $Y$ by Lemma 68.8.1 (the degree of the fibres of a quasi-compact étale morphism does not go up under specialization). Thus we may apply the induction hypothesis to $W \to V$ and find a surjective integral morphism $Z \to V$ with $Z$ a scheme, which Zariski locally factors through $W$. Choose a factorization $Z \to Z' \to Y$ with $Z' \to Y$ integral and $Z \to Z'$ open immersion (Lemma 68.9.1). After replacing $Z'$ by the scheme theoretic closure of $Z$ in $Z'$ we may assume that $Z$ is scheme theoretically dense in $Z'$. After doing this we have $Z' \times _ Y V = Z$. Finally, let $T \subset Y$ be the induced closed subspace structure on $Y \setminus V$. Consider the morphism
\[ Z' \amalg T \longrightarrow X \]
This is a surjective integral morphism by construction. Since $T \subset U$ it is clear that the morphism $T \to X$ factors through $U$. On the other hand, let $z \in Z'$ be a point. If $z \not\in Z$, then $z$ maps to a point of $Y \setminus V \subset U$ and we find a neighbourhood of $z$ on which the morphism factors through $U$. If $z \in Z$, then we have an open neighbourhood of $z$ in $Z$ (which is also an open neighbourhood of $z$ in $Z'$) which factors through $W \subset U \times _ X Y$ and hence through $U$.
$\square$
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