Jastrow derives gematria from grammateia, meaning figures in financial records, or numbers written as symbols rather than by their names. The usage in Greek fits well. You are still right in away. If one column of amounts has 3 + 4 + 5 and another has 1 + 2 + 9, the totals will be the same. Your dour informant is half right. Saying the two words have the same value is the usual way of putting it; but it is part of the gematria technique to find two words of equal value, such as snake and Messiah.
I forgot to mention before that in Jastrow’s entry for gematria you will find an attestation of an inscription in Atbash code.