What's the bargaining space in a post-doc employment contract - in the Netherlands?
Legally, as far as I understand, it is not possible to negotiate new terms that contradict the terms of the applicable collective labour agreements in the Netherlands. Many labour agreements however leave some room for negotiation, see e.g. Appendix 3 in the file you linked. In practice however there I would not expect there to be much room.

As for your example questions:


As Bill Barth pointed out, Section 1.9 arranges IP ownership, and indeed the employer owns everything. See also point 4 of Article 1.9.3. I don't see much room here for negotiation.
This is not part of the collective agreement. Your contract may have certain provisions, for example the amount of teaching (if applicable). You should discuss this with your supervisor/boss on what is expected and how much freedom you will have. Here there may be some room for negotiation.
Again, this is something the supervisor can answer. It depends on how much budget the group has available, or if your work is part of a grant funded project, how much there is available there.