I think I've only seen that theme deck packaging once. Usually, when I see the theme deck ones, there's a theme deck in its original box, a few promos, and a couple boosters.
Honestly, I've never really given much thought as to whether they should have genders or not. Though I really don't care either way. In-game, they're more collection piece than anything. I generally avoid using Legendaries now but don't tell that to 12 year old me with my BAMF duo of Kyogre and Blaziken