Because of the markup and the nature of piecing together separate templates, you'll always get invalid tags in a HTML editor. Firstly, at least in Dreamweaver, you can turn rewriting off, so code doesn't break. Secondly, I don't believe a few tags reported as invalid is an issue. The problem is the essential structure of the templates. I would often load a template into Dreamweaver and nothing much at all would display. Tables were sometimes invisible. I think most of these structural issues could be resolved if some consideration were given to widely used HTML editors like DW. My copy of GMail is still described on your site as being extensively modified, but I gave up doing that because the templates were so frustrating to work with. I was forced to edit the HTML by hand, which I am very experienced with, but I found creating the design effects I wanted next to impossible, and took to making very basic alterations instead.
Like I say, I have worked with scripts that create dynamic content. The biggest project was ecard software I designed that was pieced together in the same way as Gossamer products, ie custom tags and hundreds of templates pieced together for the final output. Displaying a template was never a problem and I used Dreamweaver exclusively. Even tables that begin in one template and end in another are not really a problem. I was able to visualise and edit template layouts in the same way as I would see them online, in the finished product. In this way it was easy to rip apart everything and redesign from scratch, to concentrate on the important aspects of graphic design, colour combinations etc, rather than being distracted by and limited to using hand coded HTML.
Jason