I notice that some applications, like the command prompt, don't use the style of the other windows. Can StyleBuilder handle the modification of those colors?
Yes. The command prompt takes on the classic look, but the rest of the windows maintain the applied visual style. These "classic" settings reside in the same place as the new visual style settings. StyleBuilder does not handle this kind of alteration nor does Microsoft. The chief reason is for application compatibility.
I have noticed that some new UI elements have appeared in Explorer. Will the first version of StyleBuilder handle those settings?
Partly. StyleBuilder can edit the Explorer bitmaps found in a visual style, but these are not used today. ResBuild or ResHacker can edit the Bitmaps in shellstyle.dll. Like most of the graphical elements in XP, these are just simple gradients defined by 2 RGB values and a series of bitmaps, some with Alpha channels.