To say that we primarily define substance this way is a bit of a generalization. The definition you used for substance is not the only definition we use today, but one of many. For example, when referring to chemistry, the definition you used is proper, but when referring to philosophy, substance has a different meaning:
The meaning of the word is dependent upon both the audience, subject, and context.
The word substance is used in this case because it is contained within and is the subject of the word
transubstantiation which is the English version of the Latin word
transsubstantiatio. It contains the following word elements:
** trans** - “to cross over, across, beyond, through, on the other side of, to go beyond”
substantia - translates Greek
ousia meaning “that which is one’s own, one’s substance or property; the being, essence, or nature of anything.”
The Greek word for transubstantiation is
metousiosis which means “a change of essence, inner reality.”
The word essence comes from the Latin word
essentia, meaning “being, essence,” (to translate Greek ousia “being, essence”) from
essent and
esse which mean “to be.”
Because the word transubstantiation itself is based on these philosophical terms and their accompanying definitions, one must use those definitions when attempting to understand transubstantiation.
Ultimately, transubstantiation explains what has happened, but not exactly how… That is the whole “mystery” part
If truly want to understand the concept and you want more info, I suggest exploring the following:
The Real Presence of Christ in the Eucharist - Transubstantiation
