If you want to make a particular Pane not to grayed out, you can add the below CSS Stylesheet to it.
JavaFX
node.getStyleClass().add("pane_opacity");
CSS
.pane_opacity:disabled .label:disabled,
.pane_opacity:disabled .button:disabled,
.pane_opacity:disabled .toggle-button:disabled,
.pane_opacity:disabled .radio-button:disabled,
.pane_opacity:disabled .check-box:disabled,
.pane_opacity:disabled .hyperlink:disabled,
.pane_opacity:disabled .menu-button:disabled,
.pane_opacity:disabled .split-menu-button:disabled,
.pane_opacity:disabled .slider:disabled,
.pane_opacity:disabled .scroll-bar:disabled,
.pane_opacity:disabled .scroll-pane:disabled,
.pane_opacity:disabled .progress-bar:disabled,
.pane_opacity:disabled .progress-indicator:disabled,
.pane_opacity:disabled .text-input:disabled,
.pane_opacity:disabled .choice-box:disabled,
.pane_opacity:disabled .combo-box-base:disabled,
.pane_opacity:disabled .date-cell:disabled > *, /* This is set on children so border is not affected. */
.pane_opacity:disabled .list-view:disabled,
.pane_opacity:disabled .tree-view:disabled,
.pane_opacity:disabled .table-view:disabled,
.pane_opacity:disabled .tree-table-view:disabled,
.pane_opacity:disabled .tab-pane:disabled,
.pane_opacity:disabled .titled-pane:disabled > .title,
.pane_opacity:disabled .accordion:disabled > .titled-pane > .title,
.pane_opacity:disabled .tab-pane > .tab-header-area > .headers-region > .tab:disabled,
.pane_opacity:disabled .menu:disabled,
.pane_opacity:disabled .menu-item:disabled > .label,
.pane_opacity:disabled .menu-item:disabled,
.pane_opacity:disabled .list-cell:filled:selected:focused:disabled,
.pane_opacity:disabled .list-cell:filled:selected:disabled,
.pane_opacity:disabled .tree-cell:filled:selected:focused:disabled,
.pane_opacity:disabled .tree-cell:filled:selected:disabled,
.pane_opacity:disabled .tree-cell > .tree-disclosure-node:disabled,
.pane_opacity:disabled .tree-table-row-cell > .tree-disclosure-node:disabled,
.pane_opacity:disabled .table-row-cell:selected:disabled,
.pane_opacity:disabled .tree-table-row-cell:selected:disabled,
.pane_opacity:disabled .table-cell:selected:disabled,
.pane_opacity:disabled .tree-table-cell:selected:disabled {
-fx-opacity: 1;
}