That could work. If it were me, I'd have the %logo apply only to having the logo on or off, and not linked to the Blog Title/Tagline at all. Because many people may want to turn off the 3-colored boxes logo, it's cute but it just doesn't fit for many niches...but almost everyone
wants the Blog Title/Tagline present. So I would make the Blog Title/Tagline a completely separate feature, and simply have 4 choices - on/off, above the header image, below the header image, or overlayed on top of the header image, with the last overlayed choice having a code box that allows you to properly position it on the image with padding & margin attributes.
I'm unclear based on your reply, are you the theme's creator? If so, I want to thank you tremendously, I use this theme more than any other due to it's flexibility. For my eBay/Amazon affiliate sites, I'm working towards creating a look very similar to Amazon.com, and so far Atahualpa seems to give me the best chance at imitating that. I also like creating my own cool headers to replace the ones Ata comes with. You can see an Ata site like this that I just did this morning at:
BTW, if you go there you'll notice I tried to assign a turquoise color to the sidebar text links, in the Widgets Tab. For some reason it only worked on the few lines of text under Laura Hanes For Women, but I could not get it to apply to the text under Recent Posts or Our Favorites, what an I doing wrong?