It is generally not known if a smooth variety over a perfect field embeds into a smooth proper variety.
Lemma 5.4 in Formes modulaires et représentations $\ell$-adiques provides such an embedding for some specific variety and this allows one to deduce the Ramanujan conjecture from Weil I.
If one also knows Weil II then the embedding is not necessary (or I guess if one knows alterations then the Weil II result follows from Weil I).
However if we keep playing geometry and forget about cohomology does Lemma 5.4 generalize in some way to Shimura varieties of PEL type?