Developers can opt in
A new Valve initiative will allow consumers to take advantage of the savings that game bundles offer without possibly necessitating the purchase of duplicate licenses. This program introduces flexible pricing -- a system that changes the cost of a bundle based on how many of the bundle's games you already own.
According to PCGamesN, it has obtained a memo sent from Valve to developers and publishers. It states in part "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."
The note continues "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."
Valve has already implemented this for its own games. For instance, the regular price of The Complete Valve Pack is $92.70; however, owning any number of those games causes the price to be proportionally dropped.
It's seemingly a program that developers and publishers can decide to opt into. When looking at The Telltale Games Collection, the price shows $174.99 for me despite owning several of the titles. So, Telltale is obviously one company that has not yet applied this dynamic pricing choice.
Although, that might be because Telltale doesn't even have the option of doing this yet. Valve hasn't officially announced this new program, instead just emailing its business partners. A few examples are up and running, but it's unclear if everyone who wishes to can move to dynamic prices. It's all very hush-hush for now. When this does eventually become more forward-facing, it'll be to the consumer's benefit, and that's always a good thing.