Is it still a rip if...
 

...I have permission to use someone's skin as a base?

Can I still submit it to Winamp.com?

so your gonna use it as a template,why dont you use the atlas

If you have permission from that person, then I'm sure you can submit it, as long as you mention in the skin's description what the original skin was, and state that you have permission from the author.

If you have permission, and include the permission in a readme.txt, then no, it is not a rip, and can be submitted.