Hmm. When I save your demo.docx sample as .odt, the R³ remains black text. Is it from the same document? Maybe make a copy of your document and delete all except a couple of equations and a little text, save (as docx). Then test that equations still save as white on white when saved as .odt and post to your question Changing colors of all formulas
I checked that a change in global font colour also affects Math (click Tools > Options > LibreOffice > Appearance and under Customisations, check Font Color. The default is Automatic). While you are there, what is shown under LibreOffice Themes?
If you open LibreOffice in Safe Mode (Help > Restart in Safe Mode > Continue in Safe Mode), open your file and save as .odt, do the formulas change to white on white?
[Edit]
I did notice that If I change Font Color as above then I need to click Tools > Update > Update all (or double click each formula) before the formulas will change colour.