To understand how just is the rule here formulated we must remember, first, that the sacred writers, or to speak more accurately, the Holy Ghost "Who spoke by them, did not intend to teach men these things (that is to say, the essential nature of the things of the visible universe), things in no way profitable unto salvation."(53) Hence they did not seek to penetrate the secrets of nature, but rather described and dealt with things in more or less figurative language, or in terms which were commonly used at the time, and which in many instances are in daily use at this day, even by the most eminent men of science. Ordinary speech primarily and properly describes what comes under the senses; and somewhat in the same way the sacred writers-as the Angelic Doctor also reminds us - `went by what sensibly appeared,"(54) or put down what God, speaking to men, signified, in the way men could understand and were accustomed to.
You're missing the point.
This encyclical is saying that the Holy Ghost did not intend to "teach men...the essential nature of things...to penetrate the secrets of nature".
But the Holy Ghost did "describe...things...in terms which were commonly used at the time...in a way men could understand and were accustomed to".
There is a difference between Teaching and Explaining something. To be taught means one has studied and knows the topic inside/out and can teach others because they are an expert. To be explained to means one understands the topic, at a general level, but not enough to teach others, but only re-explain it.
In other words, a biologist understands how a tree grows, what nutrition it needs, when to prune it and "why" pruning it at certain times is good or bad. A simple farmer won't understand the "why" but he can still understand enough to know the nutrition/pruning needs and how to grow big, healthy trees (i.e. the "hows").
The point is, Scripture and the Holy Ghost did not teach the "whys" of the earth/universe, as this encyclical says. But it did give mankind enough to know "how" to navigate, operate and work nature/earth.
So, yes, Scripture can be used to explain the earth/sciences/history (in a general sense...the "how" does it work?) but just not specifically and profoundly (i.e. "why does it work this way?").