I suspect the grey shading is due to "Field Shadings" being activated. To
disable it, go to View -> Field Shadings (Ctrl+F8). I am not a Japanese
user and can't test my own suggestion. Please let us know if it works.
Ctrl+F8 does get rid of the shading. Perfect.
Change the settings for character style "rubies", and save that to your
default template.
Alternatively, Use the ">Format >Asian Phonetic Guide" settings.
Downside is that has to be reset at every use/
It seems like this is the only way, either change the default rubies
behavior, or make a new one, but when you make a new one, it always goes
back to rubies, so the best method seems to modify the original.
Unfortunately, making the other settings sticky is impossible, I guess.
Hopefully some programmer decides to look at this area and make it better.
Unfortunately, LibreOffice with regards to using furigana can't compete with
Microsoft Word's implementation.
Thanks for everyone's help.