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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