Is there any way to reset a menu's default order (e.g. Management Menu)?
Not that i'm aware of.

It sounds like the mega menu being active is firing something like a hook_menu_alter to be evaluated by Commerce -- they've hardcoded their own ordering because its more "user friendly".

hook_menu_alter overwrites values that the menu had, so drupal has no knowledge what the default ordering was. If the mega menu is active it forces their ordering, if it isn't you get the default ordering.

You'd have to look in Commerce where they add the custom menu items, or activate the mega menu and see how their adjusting menu #weight values.

You could then write your own hook_menu_alter that undoes their changes.