See also the Ralbag’s discussion of Billam’s donkey. The point is that the Ralbag objects to Chazal’s pshat on theological grounds – not simply because he is explaining a different level of pshat. In the cases of Billam and Lot’s wife he is disagreeing with Chazal on the theological implications of miracles (under certain circumstances), and in the quote from Bereishis he is disagreeing with them about changes in the ratzon Hashem.
If you are interested, I recommend reading the article entitled “The Scholar Rabbi Levi – A Study in Rationalistic Exegesis” by Yitzhak Grossman in Hakirah vol. 12 available for free download on their website.