The costs are compiled from the NET change of the levels on the "new" list in comparison to the previous list of enchantments on the item. 
Then, each individual enchantment's cost is calculated and summed up to determine the total cost:

1. Start off with the initial base cost (Set by config, default 35 experience points).
2. Multiply the cost by the "Weight Factor": 11-(enchantment weight) * (config's weight factor); must be at least 1. See https://minecraft.fandom.com/wiki/Enchanting for weight listings.
3. Multiply by the net power change. 
4. Multiply by config's "costFactor"
5. If curse or treasure, multiply by respective factor from the config (default curse: 3.0. default treasure: 4.0)
6. If curse & taking levels off this specific enchantment, divide by receiveFactor to bring price of taking it off up.
7. Apply the enchantment's personal factor and personal receive factor as set by config if exists

Each enchantment's cost is ALWAYS summed up then, unless "takingLevelsOffXP" is false in the config. Then, taking levels off (net level change is negative) is substracted from total cost instead of added.

1. The cost is the amount of damage the stack contains.
2. The repairFactor from the config is applied. 

You do not get a discount from just bookshelves: you must build the dark shrine.

IMPORTANT: you don't have to build the entire structure, just the inner crying obsidian ring & the initial bookshelf ring. 

Please see our github article explaining the steps for building it: 

https://github.com/frqnny/dark-enchanting/wiki/Dark-Shrine---How-to-get-Discounts-with-the-Dark-Enchanter