“Charlie, You cannot apply the Aggadaic rule to the Torah.”
I never said to do so!
“The Torah was given to be understood, and it was understood a certain way for 3000 years.”
This is misleading. Rishonim came up with novel understandings that had no precedent in Chazal. Even some Acharonim came up with novel understandings.
“How to reconcile the Torah’s description with science’s findings is up to you.”
This is correct; there is no chiyuv to believe any particular reconciliation. Reconciliation is not something that particularly troubles me.