First of all, it's not the clearer divs which cause the problems, its clearing floats. If you get rid of the clearer divs then you will have to find an alternative method of containing floats or your forum will just collapse in a heap (except in IE). The method I'm using now still uses clear:both, it just does it without needing an empty div.
Before I struggle with it on my own, mind if I ask you a quick question?
The problem is, with my site, that before the content of the page there is a nav system that I am floating left. So when punbb clears both, it makes the punbb block that cleared extend the whole height of my nav system, which is totally unacceptable.
I couldn't think of a way to modify my layout (I use to absolutely position the nav, but I had to float it so that the footer of my page would always stop at the bottom of it (with some negative margin and clear magic)) even if the content was shorter, so thats why I was looking at modifying punbb's layout instead.
Its all fine if your just using punbb by itself, but if you are embedding it within your sites design, that can cause headaches. Many complex css layouts use floats to accomplish their magic.
As for the markup changes, they are more significant than I first thought. Basically I've been deleting stuff from the markup and adding more css. Yes it will be a headache to update your stylesheets.
Alright. I'm all for improvements, so its OK by me. I figure since by the time 1.3 comes out my actual forum will be running already, I'll just give myself a test 1.3 environment to tinker with till I have it the way I want it.