Still being two moves away from castling, the opening of the e file would create problems for Black, that's why in the Open Spanish and the Berlin against Nxe4 the most energetic move is d4. It is superior to the immediate Re1, because in the open Spanish Black has Nc5 hitting the Ba4, and in the Berlin Nd6 hitting the Bb5 again before White can use the e file (5. Re1 Nd6 6. Nxe5 Be7 and Black is in time to cover the e file so it's ok for them).
As for the problems the e file creates for Black, there is a long theoretical line in the Open Spanish starting with 4. Ba4 Nf6 5. 0-0 Nxe4 6. d4 exd4 7. Re1 d5 8. Nxd4 Bd6 where White ends up with the better position. Black faces similar tactical problems in the Berlin after 5. d4 exd4.
i don't know though if you are talking about something else with 5..nxe4 since in the berlin black takes on move 4. i think in the open spanish he takes on move 5 after white castles so maybe that's what you are referring to.