For example, in the table where first node spans two rows, it should be possible to fill three nodes as following:

GridPane.setRowSpan(spanNode, 2);
gridPane.addRow(0, spanNode, node2);
gridPane.addRow(1, node3);

so that node3 goes into second column because first is occupied by spanNode.

This is logical as javadoc for addRow method is saying the following: "If the row already contains nodes the specified nodes will be appended to the row." Unfortunately, it doesn't currently account for nodes that span from other rows/columns.