That ruling is only applicable to pack-in games. This one you are posting about is an entirely separate situation and doesn't apply to that. Because as you are showing, the internal components (boxes) are not 2 games, but they are 2 discs.
A similar situation for this would be The Pandora Directive, which has an outer box and inside are 2 jewel cases because the game has 6 discs. The two jewel cases inside are not allowed separate entries, just the main box. So this Gamecube game should only have an entry for the outer box and not the individual boxes that are inside. In the description you put the info for all the stuff inside the box.