The exception you're describing is where the employer is hopelessly naive and unknowingly signed and gave me a contract they didn't read with horrendous terms, and they're very apologetic when I ask them to amend it.
Well, that actually happened to me once.
I thought everything was fine when the terms were amended, but the guy who hired me was still hopelessly naive.
That ended up SERIOUSLY coming back to bite me in the ass as he ran out of money, panicked, hid himself and didn't tell anybody what happened. Eventually he told me that he ended up not paying me because he couldn't.
He was a nice guy and he plainly felt awful, but that wasn't much consolation to my bank account.
So yeah, the when there's a possibility you're negotiating with somebody who is either hopelessly naive or evil, I don't really care which they are. I don't want to work for them either way and neither should you.
In general the ones who intentionally put the clauses in weren't necessarily the most awful places to work in the world, but none of them were job opportunities of the lifetime, and I wouldn't have felt bad passing any of them up.
I have drawn lines through the objectionable parts of employment agreements, initialed my changes, and then sat patiently while the HR people freak out. It has usually worked out happily for all concerned, not counting the people who think the employment agreement is a gift from their god and must not be altered by mere mortals. When those people have enough power to reject my rejection, I'm happy to walk. But it's important to verify that they have that power, IMHO.