The Ibn Ezra's "valid" approach for solving difficult verses

The post about the problems with Noah's flood, and how Orthodox Jews should address them, produced some great dialog.What follows, is an example

A Guest Post By YEEDLE
When I first read  DovBear's post about how he reads the flood story I was skeptical. I never heard of the Rav Se'edyah Gaon you quoted, and I never thought that such a line of thought was ever accepted by traditional Judaism.

DB: To review the reference is to Sa'adya Gaon in Emunot v'Deyot 7:2 where he says there are four conditions under which the Torah is not to be taken according to its literal meaning (1) When the plain meaning is rejected by common experience, or your senses; (2) When it is repudiated by obvious logic; (3) When it is contradicted by scripture; or (4) When it is opposed by tradition. Though Sadya Gaon wrote this more than a thousand years ago, his position is not well known among "traditional" Jews. 

I was shocked into realization when I came across the second version of the Iben Ezra's commentary on Parshot Breishit, Noach and Lech Lecha.

In the introduction to the second version, IE writes about five approaches to interpreting the Torah. The first three (which he calls The Christian Approach, The Tzdokim's approach and The G'eonim's Approach) he denounces.

The other two (one of which is The Talmud's Approach, and the other his own) he praises calling each a "valid" approach. In explaining the Talmud's approach he raises an interesting point. Let me quote him:

הרביעית, היא דרך סלולה לקדמונינו, היא הרשומה בתלמודינו ... כי פעם יפרשו הכתוב כמשפטו על דרך פשוטו, ופעם ידרשו בו דרש לסוד עמוק או מפורש.

והנה אומר כלל בתורה, גם בדברי המקרא גם במשנה, ובכל מסכתות ובכל ברייתות ומכילתות. שאם מצאנו באחד הנזכרים, דבר שיכחיש אחד משלשה דברים, כי האחד שקול הדעת הישרה, או כתוב מכחיש אחר בסברה, או יכחיש הקבלה הנגמרה, אז נחשוב לתקן הכל כפי יכולתינו, או בדרך משל, או תוספת אות או מלה על דרך לשונינו. ואם לא נוכל לתקן אל האמת, נאמר כי זאת החכמה ממנו נעלמה, כי יד שכלנו קצרה, ודעת בני דורינו חסרה. ... וחלילה לנו לומר שהוא שקר וכזב, גם לא נאמין שהוא כמשמעו, רק נאמין כי הכותב זה הסוד ידעו, כי יש בדברי הקדמונים סודות, על דרך משלים וחידות, שלא יבנום כל השומעים, ולבעל המחקר יהיו נודעים.

In English:

A rule regarding interpretation of Torah, Mishna and Chazal: Whenever you find something that contradicts one of the 3 following: common sense, logic, or our Mesora, we have to reinterpret, either in an allegorical fashion or by adding a letter or a word. And if we can still not interpret the passage in a way that it doesn't contradict the aforementioned three things, we won't say that the passage is untrue and false, but neither will we say that it has to be taken literally. But we will say that there is a secret that our shortness of mind can't grasp, and it was written in such a way that only those who have to understand should get it.

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