I'm wondering if anyone has checked their Atahualpa or TF sites for code compliance at http://validator.w3.org How clean is the code these things write?

I'd consider the code to be very compliant however you should keep in mind that in some cases accepting an W3C "error" on purpose can actually be wise. W3C does not care about browser coverage at all so sometimes you'd either have to use Javascript (which W3C does not check for/detect) to fix a browser issue or do it with a lightweight CSS "hack" that W3C will complain about.

Ultimately real world browser coverage is the most important in my opinion. That doesn't mean that W3C is ignored, but I suggest that even if there are "errors" one should have a closer look at what kind of errors these are.

Also, HTML5 is still a working draft (and might be until 2013/2014), so, as far as HTML5 elements are concerned the W3C results should not be taken too seriously. W3C actually says that themselves somewhere on their site.