I've just encountered RT-15137 again which is in fact reproducible when 3D transform is added via dynamic animation.

So next line from the attached code:

                System.out.println("Zero Volume bounds: " + ellipse.localToScene(new BoundingBox(0, 0, 0, 0, 0, 0)));
                System.out.println("Unit Volume bounds: " + ellipse.localToScene(new BoundingBox(0, 0, 0, 0, 0, 1)));
                System.out.println("Zero Volume bounds: " + ellipse.sceneToLocal(new BoundingBox(0, 0, 0, 0, 0, 0)));
                System.out.println("Unit Volume bounds: " + ellipse.sceneToLocal(new BoundingBox(0, 0, 0, 0, 0, 1)));

produce the following output:

Zero Volume bounds: BoundingBox [minX:227.0, minY:274.3748474121094, minZ:0.0, width:0.0, height:0.0, depth:0.0, maxX:227.0, maxY:274.3748474121094, maxZ:0.0]
Unit Volume bounds: BoundingBox [minX:227.0, minY:274.15263194001614, minZ:-6.5307251029356195, width:0.0, height:0.22222922625132924, depth:0.9749944466506975, maxX:227.0, maxY:274.37486116626746, maxZ:-5.555730656284922]
Zero Volume bounds: BoundingBox [minX:-2270.0, minY:2687.486328125, minZ:0.0, width:0.0, height:0.0, depth:0.0, maxX:-2270.0, maxY:2687.486328125, maxZ:0.0]
Unit Volume bounds: BoundingBox [minX:-2270.0, minY:2687.486116626751, minZ:54.5823121161985, width:0.0, height:2.222292262513747, depth:0.9749944466506975, maxX:-2270.0, maxY:2689.708408889265, maxZ:55.5573065628492]