Hey @Vixi, welcome to the forum and thanks for your question!
I can’t figure out how to use Japanese phonetic guides in Collabora Online […]
You can’t as of right now (Collabora 23.05.3).
But, if you give a little more info in how you use + insert these phonetic guides in LibreOffice, it could help get this feature added! 
- How do you insert Phonetic Guides in LibreOffice?
- Do you have any sample documents with Japanese + ruby text inside?
In LibreOffice, according to:
it also looks like there’s a menu under:
- Format - Asian Phonetic Guide
which appears after you:
- Go to Tools > Options > Language Settings > Languages
- Enable “Asian”.