You don't need to get rid of windowbg everywhere.
I think we need to have a 'generic' class for areas that need to apply a background, whether striped or not, but I don't really know... Just 'bg', maybe, would be fine..? But form vs. function, etc... So, just 'window' or 'win'...? Well, 'windowbg' never really made sense, I mean, it was never about 'windows', more about simply areas with alternating colors, so... 'zebra'? No, we need to ensure that the class can also be used on non-alternating areas, hmmm...
One at a time - there's already postbg specifically for posts, target that first. Then one for the thoughts list, and so on and so on. Eventually yes, windowbg will go and that's a good thing. Ideally each major area should have its own set of classes so that it's easier to style at will - while it will take slightly more CSS, the per-page saving could be surprising - because you wouldn't necessarily need to leave in all the classes; I don't know what 'root' does but I see no reason why you couldn't flatten down 'root postbg(2)' to simply postbg,
There are precisely two XenForo sites I know of that don't look like XenForo. Every other installation just screams XenForo. Ditto for IPB. Anything that introduces behaviour that is dependent on rewriting layout markup is going to be fragile.