With patience and tact, is how I respond to this. I know, I can explain to my students three or four times how I would like their homework turned in. I tell them, put your name just here, place it face-down with the top towards me. I get it folded in half with the name on the outside, I get it folded in half the other way, I get it with the name in the middle, and more variations than I could shake a stick at, if indeed I felt like shaking sticks. In one ear and out the other. Sigh.
I have a similar problem with homework. I give some credit for homework to encourage the students to work the assigned problems. I make them put it in a spiral notebook, table of contents, and the pages numbered. I used to have a problem getting a number of students to do something so easy.
I think the problem is that students typically see the issue only from their side (the same can go for instructors, too!) and when they deviate, they don't see it as a big deal. So what if the student turns in the homework on looseleaf paper? They don't see it as a management problem for the instructors and it's the reason we all have various policies. We need to manage the load.
I explain this to the students on the first day and tell them that if they don't follow the homework policies, they will get no credit for the assignment. Their homework notebook is turned in every week or so and I take a couple of minutes to scan their work. The first time it's turned in, I take a set number of points off if it isn't done properly. After that, they get nothing.
My dean used is also a math instructor and he told me how he handles the same problem you describe. If they don't do it a certain way, they get nothing.
Tact and patience is fine as long as you set limits for typical situations.
As to the op's post, I keep all emails and use them for "difficult" students. Make sure things are clear and try not to take offense. I had a student a few quarters ago who was very rude in a number of emails. He eventually was given permission to do a late withdrawal because his mother had been recently diagnosed with cancer and he had to get a third job to make more money to help his mom.
Alan