Also, other things (i.e., vacations first 6 months, or some small perks) mention only after you negotiated the salary and pretty much you close the deal.
If you frame your counteroffer as “I would take this job if you gave me $X more base salary or Y more vacation days”, then the guy across the table can decide which option is more offensive to company policy. It’s not your job, as the applicant, to decide in advance what terms the employer will accept. Your job is to communicate what you want until you either have a deal or feel comfortable walking away from the table.
At worst, you're just going to look like an entitled asshole from day one if you try to get special treatment.
Personally, I have better things to do with my time than count up how many days off each of my co-workers have taken and compare them with the numbers in the employee handbook.
Those policies are there for people that don't choose to negotiate those terms.