Before the Romans, the Greeks were already using phonetic letters as numerals. They did saw Iota as either a number or a phoneme depending on the context.
Looking at these older sytems, it looks like the romans just mixed both approaches, either on purpose or not. (I have absolutely no evidence to support this, it's a guess).
We know the Romans were influenced by the Greek, and the Greek by the Minoan.
Both the Greek and Minoan had their own numerals:
https://en.wikipedia.org/wiki/Aegean_numerals https://en.wikipedia.org/wiki/Greek_numerals
Before the Romans, the Greeks were already using phonetic letters as numerals. They did saw Iota as either a number or a phoneme depending on the context.
Looking at these older sytems, it looks like the romans just mixed both approaches, either on purpose or not. (I have absolutely no evidence to support this, it's a guess).
Maybe the problem is really older than we think?