Steam is to make a change to how it prices all of its bundles, and will be adopting a pricing model that looks at whether or not you own a game featured in bundles. While this hasn't been officially announced, Valve sent out documents to developers detailing the new system, which PCGamesN have obtained.
This essentially means that if you already own a game in a Steam bundle, the price will now go down instead of you just not getting the game. This changes depending on how many games in the bundle you already own. The leaked document gives more details:
"With Steam Bundles, if a customer already [owns] some items in the Bundle, they will pay for and receive only the items not already in their account. This allows the best fans of your series or franchise to 'complete the set' and get a deal on the remaining items in the Bundle."
Valve goes on to say that if players saw that they already had a game in a bundle, they would be less likely to buy the bundle even if it provided a better deal:
"Past Complete Packs were sometimes a bad deal for customers that already [owned] one or more of the products in the pack. Either it made bad economic sense for those customers to purchase the pack, or they just felt bad about doing so since it [looked] like they were paying for products they already [had]. The new Steam Bundles system addresses this."
This new system has already been put into place - The latest bundle on sale on steam, the Headup Games bundle, incorporates this system and changes the price accordingly.