Why he didn't think of this is beyond me but then again, he's not mean or nasty or...me.
Here's his problem: he asks people to paste their query letter into their manuscript when sending a partial or full. Most people do it. 1 in 4 do not. Nathan posted a plea on his blog for actual queriers to help him make the wording clearer. He thought maybe people just didn't understand.
Here's what I do when people don't follow the directions: send a reply saying "please resubmit your requested manuscript and this time follow the directions."
I don't do the cutting and pasting for them.
I don't explain the directions in different words.
I also don't discard the query.
One mulligan per query...but that's only for partials and fulls.
If you don't follow the directions at the initial query stage (send your query as an attachment; don't tell me what the book is about; cc or bcc every agent in NYC) I don't worry about it. I just say no.
The horrifying fact that 25% of the pool either missed seeing or just didn't follow the directions doesn't surprise me in the slightest. Somebody has to be below average! I just hope it's not you.