Thanks!
This is definitely something I would like to improve. Right now, the game only allows for one sequence of ascii characters to represent a chunk of text. These are manually defined in the word lists. I just chose the romanizations that I'm personally used to typing on the MacOS IME.
It's probably #1 on my list, but I don't really have a design in mind to fix it at the moment. I don't know if it's possible to make every user happy here, or if some sort IME settings screen would be needed.
The constraints I have are that I'd like for the game to continue to be compatible with non-Japanese languages, and I would like to make it easy for users to use their own word lists in the future.
Feel free to create a github issue, and we can move some of this information there. I've gotten a bit busy recently, but I'll have a bit more free time soon and would be very open to collaborating on this.