With the Merchant 5% maint. cultural bonus and Maintenance set at 120. You are now paying, 25% - 25% = 0% maintenance.
With regard to your suggestion. If a ship costs 1000 minerals, and you want 120 maintenance to mean that you knock off 20% of 1000 from the maintenance, this lowers the maintenance of the ship from 250 minerals to 50 minerals or 5% of the cost of the ship. This is how it currently works.
Choose the Merchant culture for the extra 5% maintenance, and you pay 0% maintenance...