Drop a Button on Content and look at CSS Analyzer (configured to hide properties with default values).
See attached LabelPadding.
When I save such a layout the FXML file contains for the button:

</Button><Button mnemonicParsing="false" text="Button" />

There's is no mention of some padding.
It is confusing to have padding value in Inspector column of CSS Analyzer if it doesn't read in the FXML file. Possibly it is the persistence code that skips it given the value is the same as platform default one, but that doesn't prevent confusion.