Hmm... yes I just ran my example on a dupe oto.ini so as not to ruin the real thing if it goes horridly wrong >.< and it would have, lol.
There are a number of Japanese characters whose romaji equivalent would match a few search strings, such as
matches all three of these search strings:
So how could confusion be prevented in this matter?
The reverse is not totally true, the same example (but instead from hiragana to romaji) would not have many issues:
does not match
Though they are the same in reverse.