The XSSFPatternFormatting class does not include setFillForegroundColor and setFillBackgroundColor methids that take an XSSFColor parameter.. Thus, conditional formatting can only used IndexedColors
This has hopefully been solved with bug #58138, as XSSFPatternFormatting now additionally accepts XSSFColor objects for its colour setters Would you be able to check a nightly build / 3.13 beta 1 once released, and confirm that your use case is now covered?
Setting to fixed as it should work and there was no response for some time.