Remember there are two "format" options - one for the schema compare itself, and one for the side by side viewer. You may want to turn them both off.
In Schema Compare, it's on the "Choose Options" step. Click 'Options -> Objects' on the left, and then on the right, under "PL/SQL Objects and View Source", uncheck "Format before Comparison".
In the side by side viewer, click the last toolbar icon, then in the dialog that appears, Options -> General on the left, and uncheck "format source before comparing" on the right.
There is an option to control the comparison of row movement.
In the Schema Compare window, on the "Choose Options" step, click on "Storage" on the left, and then make sure "Row Movement" is checked. It's the 2nd to the last item in the list.