In my experience the problem is that these clauses are traditionally presented to you by a non-technical employee typically from HR, and (in my anecdotal experience) these employees usually try to dismiss your concerns with a "oh it's just a formality" or "all companies make you sign this sort of thing!"... so if you're not important enough to talk to someone higher up, you might just get your offer revoked if you try to fight it because your HR contact isn't important enough/doesn't care enough to fight against it for you, and the legal department only has so much time for custom agreements.
-Agreed that the clauses are most often presented by someone not authorized to waive them.
However, I've found on the couple of occasions where (non-reasonable) NCAs were presented to me that simply claiming that the terms as stated are not acceptable and that a revised NCA must be prepared if I am to sign it results in a shrug and a 'Whatever. We'll just skip it, then.'
Now, if they'd stood their ground, I'd have had to look elsewhere. (I am not a big fish - just a lowly engineer who do some management on the side - so they didn't waive the NCA for REALLY wanting me to come aboard; more from reluctance to go through all the hassles of either doing another hiring process OR amending the NCA.)
(At a former employer, the NCA basically stated that anything I ever thought of, be it at work or after work, in my field of expertise or in whatever unrelated field, belonged to them. Oh, and this obligation extended past the termination of employment for a period of time decided at their discretion. Not enforceable in the least, but still...)
Oh I do. I'm just saying that most folks aren't as stubborn as me, and it's unfortunate that you have to play games over something like that. All it does is screw over people who don't have many options, and widen the delta between the haves and have-nots in our field (the haves have the luxury of rejecting these clauses, while the have-nots might not be willing to "roll a hard 6" on their only job offer).
You have just been hired as their new rockstar developer. If HR lose you over this HR will be taking some flak.
Just speak to your future line manager and explain that you have returned a modified version of the contract and that you hope that they will agree to it soon because you are really excited to start working.
If someone doesn't have the power to change the contract, then they don't have the power to negotiate with me. And if they don't have the power to negotiate with me, then what business do they have offering me a contract to sign?
This is why the solution to this kind of problem is industry-by-industry collective action. Once 10 people in a row tell the HR person that they're not signing that garbage, even the densest bureaucrat will take notice.
At that point HR wasn't the one making the decision to hire you, simply because HR isn't qualified to evaluate an engineer after initial screening. At least companies that actively try to find good engineers for their roles, HR is in no position to withdraw an already given offer by themselves.
