Are you telling me that I should somehow not apply any theme globally and instead apply an individual theme to each individual application?
No, I said you need to apply a theme, any theme, you wish to use. Except Default theme, which, if you do will disable Windowblinds.
Are you telling me that WB cannot modify the appearance of the windows for any of these applications in any way?
No, It can change it. Just that if your main theme change the Windows system color, this usually happen in a dark theme, where they, the Theme Author, change the Windows Background color to black or something dark. This change system color will be used by any other program that use that Windows color. For example if the Windows background color is set to be black. Program like Excel, Word will have black background too. Which will not work for some people.
As for appearance, yes it will change those other application to any theme you wish. if you set it correctly.
I am primarily interested in changing the color of the title bar on a per application basis.
I believe, it is possible. Refer to my s/shot below I set 3 application using 3 different theme.
Stardock Community Assistant.