There're couple of questions alerady on SO, however since JPMS support none of the answers are valid.
method 1: (JavaFX - Set default CSS stylesheet for the whole Application)
Application.setUserAgentStylesheet(Application.STYLESHEET_MODENA);
StyleManager.getInstance().addUserAgentStylesheet(getClass().getResource("/style.css").toString());
Doesn't work because StyleManager became the part of private API and JavaFX doesn't export it.
method 2: (https://stackoverflow.com/a/51003008/7421700)
@import "com/sun/javafx/scene/control/skin/modena/modena.css";
/* rest of CSS code */
Doesn't work because modena.css became the part of private API and JavaFX doesn't export it.
method 3: set CSS to the top parent node (https://stackoverflow.com/a/28880421/7421700)
Doesn't work because CSS will not be applied to modal windows.