Thanks for posting your question. I'm more than happy to assist you today. Yes, as vps servers have few limitations, VPS customers can brand their servers with custom CSS. This is all accomplished by using WHM. Webmail uses the same CSS as cPanel itself, so once cPanel is branded - the effects will carry over on webmail as well.
If you need further assistance please feel free to contact us.
I spent a little time researching this and asked a systems person as well. The systems suggested the same file that you're reviewing -webmaillogout.cgi, but we have no specifics. I also found some discussion of the same issue on cPanel's forums (the people who provide the Webmail interface), but again, I did not see any specific solution. You may need to contact cPanel and see if there's any documentation available that lists the file and if its possible. I do apologize for not getting a clearer answer, but here's the link for the forum posts that I saw on the subject: cPanel Forum posts on webmail issue. These are older posts, so there may be some newer information available. If I do run across anything, I will re-post to this comment and update it.