This I do not understand. If the <div>, which I assume means the entire gallery, is centered, and then each element is centered within its own area, why does the Main Image have a greater amount of blank space on its left side than its right, if the edge of the thumbnail is assumed to be the edge of the thumbnail container?
Take a look at this screenshot using Firefox's 'Inspect Element' functionality. The dotted line shows the thumbnail area. The area to the right of the thumbnail area is the image area. The thumbnails are horizontally centred within the thumbnail area and there is an equal amount of space to the left and right of the main image within the image area.
Why is the Button Bar not centered
This is caused by a bug (buttonBarHAlign="CENTER" does not work when thumbsPosition="LEFT" or "RIGHT") which has already been addressed and will be fixed in the next version of Juicebox-Pro.
Why would the thumbnails be flush to the edge of the container, if the entire gallery is centered within the container?
Setting thumbsPosition="LEFT" (in conjunction with thumbPadding="0" and thumbNavPosition="BOTTOM") will automatically have the thumbnails flush to the left edge of the gallery. My suggestions above will allow you to move the thumbnails away from the left edge of the gallery.
Centering the gallery (the 'juicebox-container' <div> with the background color of #63000) within your page (so that there is an equal amount of space either side of it) is different to positioning the gallery elements within the gallery.
I want it, along with the thumbnails, nicely aligned center.
From the mock-up screenshot you provided, it looks like the layout you are after might be achieved by simply increasing the value of the stagePadding configuration option from its default value of zero, e.g. stagePadding="50"