E.g. "I'm very interested in the position we discussed, but would like to discuss clauses X, Y, and Z. These pose a problem for me for reasons. If this is something you could be flexible on, I'd love to see what we can agree on! If these aren't clauses that can be changed, I feel that salary +A and benefits +B would be more in line with what you're asking for."
If phrased like that, you're putting the "choice" back in their hands, but making it clear just how much these things are worth to you.
They may say "Neither of those options works for us," but the difference is that they're making the decision to torpedo your hiring over one of their own clauses. Imo, it's much more difficult to say "These clauses are worth A & B" than it is to say "These clauses are super important."
Much harder to do this in a bureaucratic company that has been around forever since they tend to be pretty inflexible on everything except salary/benefits.