I think they are two totally different concerns here:
1) People want the (horizontal) Category places on the Left/Right hand side with the exact same function - this is no the same as creating another Left Nav that has the flavor of Layered-Nav that uses attributes and filtering.
2) People want the Vertical Category in the (CMS) Homepage
It seems that Justify wants the #1. I think this is easier and only require to modify the CSS (just the #nav in the menu.css) and re-arrange the block of top nav in Page.xml, catalog.xml and maybe default template too (haven’t look into this issue closely so I maybe missing something).
I suggest you read the newly updated Designer Guide.