Romaji2Hiragana is a plugin script for MuseScore3 which converts romaji like 'ra' and 'to' to 'ら' and 'と'.
Set the lyrics of your composition in MuseScore3 to romaji. Then just run the plugin and it'll do the rest.
I didn't put a lot of time into this, so if you have any issues just let me know and I'll see what I can do.