Problems of Amending Contracts
Consider the entire exchange from the view of the editor. You mailed a contract to a writer, received a signed copy, and put it in a stack to file. Your days are busy and you spend a week or two on deadlines. Eventually, after editing the article that the writer had sent and getting it ready for the next issue, you are doing some filing and come across the contract. Just before you forward it to the contracts people, you notice a pen mark. And another. And others. You've spent significant amounts of time on your end of the assignment only to realize that the writer isn't willing to work under the terms you had thought were set. Now everything might be up in the air, all without enough time to recover and find another writer or another article.
Take it a step further. The signed version shows up directly at the legal department, which then calls you and asks why you authorized all these changes to the contract without talking to someone there. The writer has just gone from an inconvenience to someone who is damaging your professional reputation.
Back to being the writer. The editor should have noticed the changes at the start, but realistically it could easily happen that no one would see your demands until late in the game.
Why do many take this approach? Because they are afraid of confrontation and hope that by sending an amended version, their demands will sneak by and they won't have to talk to someone. Although this might work on some occasions, it's ultimately self-defeating. Each time you act from fear, you reinforce that feeling and response. The next time you get a contract, you're that much more likely to change, sign, and send and hope that it doesn't come back to haunt you.
Some argue that by mark up the contract and sending it in, you're legally declining the terms and counter-proposing another set, so that if the publisher uses the piece, those would be the terms covering the relationship. That might be technically right, but it's still a way of thoroughly screwing yourself. You are always, always, always better off contacting the editor regarding any terms and conditions that you find unacceptable. The editor might not be able to make the changes or might. Or the editor might be unable to bend on one issue and instead offer something else - possibly more pay or something else important - to make up for it. Even if there is no other reason at all, talking or emailing the editor with your concerns and what you're seeking helps you build a relationship, and it's the relationship that can become a steady income stream, not the piece of paper that the company overlooked and is now forced to accept.
Update: one more consideration here.