YHWH is a late development in Israel's worship, and has been retrojected into the text of Genesis (usually in place names that had it incorporated by the time of the Return) by the post Babylonian Exile Priests etc who produced the Scriptures for the fledgling nation, as the returnees in fact were, even though they had a history in the land.
If Noah were not simply a fictional character, as I am sure he is, then, at the time he supposedly lived Yahweh was unknown. Yahweh was taken over by those Jews from circa 537BCE as the national God, of a nation that they wanted to be monotheistic.
Before adoption by the Jews, Yahweh had a chequered past, having a wife/consort for example, there have been a number of threads on this.
The God El maybe predates Yahweh, certainly El predates any idea of Yahweh's supremacy, so El would be a better choice out of the two.
The Director's idea on this makes much more historical sense than adopting a name which came much later than the supposed setting of Noah.
Will there be a Noah 2 movie, subtitled "Oh bugger, its raining again" ?