Gold is an element because God created it as gold; it was made directly by God.
But a precious stone has been formed from various kinds of elements, which have been composed together through chemical combination through countless years of heat and pressure in the earth.
In other words, the precious stones do not signify something given directly by God, but something which the Holy Spirit has produced in man by much effort and many years of burning.
The work of the Holy Spirit on earth is to continually put us into trials so that we may have all kinds of experiences and become precious stones before Him.
The precious stones, therefore, are the product of our being disciplined by Him.