Ask your DM
In this case, the DM is coming up with a system for pricing. We really have no idea what that system is and you need to discuss it with them and work out the kinks and interactions you're interested in.
The DMG (page 135) has a chart for pricing ranges across the various levels of rarity for magic items.
If your campaign allows for trade in magic items, rarity can also help you set prices for them. As the DM, you determine the value of an individual magic item based on its rarity. Suggested values are provided in the Magic Item Rarity table. The value of a consumable item, such as a potion or scroll, is typically half the value of a permanent item of the same rarity.
Unless you decide your campaign works otherwise, most magic items are so rare that they aren’t available for purchase. Common items, such as a potion of healing, can be procured from an alchemist, herbalist, or spellcaster. Doing so is rarely as simple as walking into a shop and selecting an item from a shelf. The seller might ask for a service, rather than coin.
The pricing ranges are the prices for those items, it doesn't say that they are in addition to the mundane cost for that type of item. The DMG just provides the range for that item.
More optional guidance in Xanathar's Guide to Everything
Chapter 2 of this book has some additional pricing options. These are likely all-inclusive because there is no language of "add this cost on top of the mundane price for the item."