Displaying the custom taxonomies side by side on the admin dashboard

Have you tried using CSS to affect the display when they are in the main column? That seems like the best solution to me. The main problem is that the actual layout of the box changes when you move them into the main column to use the horizontal space better (tabs at left instead of above list). You’ll have to reverse-engineer all the CSS that changes the layout to make it behave like it does in the sidebar.

Either way it will probably be a pretty complicated chunk of CSS, and will need to be reviewed in the future when the styles that define the default behavior are changed.