Well, in fact, we cannot really say that indent() works only with left alignment. I'd rather say that it seems to work a bit differently when using right alignment.
The notion of indent is just extra space added on the left of a row, or more precisely, as mentioned in the javadoc, space added before the left most component of a row.
In the case of grids, the labels in the label column (the 1st column of the grid) are, initially, all forced to the same width (the max width of all labels in the column). Then extra space is added when rows are indented.
When you use right-alignment, the indent space most often won't clearly be visible to the end user.
However, there are situations where this indent will appear as expected:
layout.row().left().add(new JLabel("Address"), new JSeparator()).fill();
layout.row().grid(new JLabel("Street 1")).indent(1).add(new JTextField("Benjamin Franklin Bd"));
layout.row().grid(new JLabel("Zip Code")).indent(1).add(new JTextField("CA 1234"));
In the example above, when using right alignment, you will see that "Zip Code" is indented in comparison with "Address". You would see no indent at all when not using indent(1).