There are lawyers who do this type of negotiation.
> HR/hiring people will look at you like you're some kind of weirdo if you balk at any of it. Here are the reactions to my reluctance as I recall them.
Right. Go over them. Your lawyer will talk to their lawyers, above the level of the HR people you would be talking to.
> I didn't want a contractual responsibility to come and defend patents in courts,
Which is a pretty reasonable requirement...
> or give depositions at my expense.
But that is not (or, rather, it can be in certain circumstances).
A good lawyer will negotiate these things for you. You should try to find one who actually understands software a bit. They do exist.
Disclaimer: I am not your lawyer. If you need a lawyer, you should get one.