I wrote stand-alone papers for my dissertation, too. I thought it was good training in the art of writing a publishable paper. (And because I went straight into teaching in a temporary job, rather than getting a post-doc, it was the only training I ever had. Otherwise, I would have been learning a new writing style without the benefit of constant discussions with my committee members.)

My grad advisor, though, questioned whether it was a good approach. I think she kind of liked the old tomes, and there were things she wanted me to say that weren’t really defensible to our most likely reviewers. (Actually, the comments you’ve received sound like something my grad advisor might say at random during Friday Beer…)