Thanks for the vote of Gumbo confidence.
With regards to malformed code, you are literally taking a greater risk by leaving it unchecked than you are by checking it. I know people are still gun-shy from the days of htmlTidy, but it really is true.
I would only consider unchecking it if I was opening markup that I was intimately familiar with and 100% certain of. And in that case ... there'd be no reason to turn it off since nothing would get altered anyway.