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I’ll second that. I once decided to refactor a cms (I think it was Concrete5) to output html4.01 strict instead of xhtml… I worked on it for three weeks, completely broke the system a dozen times, and eventually decided it didn’t really matter. Either use something the way it was designed, or make your own.

If WP is outputting valid, cross-browser markup (type="text/javascript" won’t hurt anything), then don’t worry about it.