Squeak,
You are correct in your explanation. Tosafos themselves, regarding Pi, say that 1/3 of circumference is imprecise, but, since the whole din of koreh is midivreihem, they did not wish to encumber people with exact measurements, and, if one measures a beam to be 3 t’fachim around, he can assume, as far as the halacha is concerned, to satisfy the requirement of a tefach’s thickness.
The Rishonim, furthermore, explain that the various shiurim for Deoraysa mitzvos were also given in imprecise-by-definition measurements of kezais, amah, etc, to enable every Jew no matter where to observe these Mitzvos. Not only aren’t all olives equal, but those of one land will differ from the ones in another, yet, consuming a local olive’s size measure of Matza will satisfy the halacha, and eating the same shiur of chelev will make one chayav chatos.
One should not confuse Chazal’s deliberate imprecision in regard to measurements needed for daily observance with lack of knowledge in natural sciences.