My understanding is that bundles just give access to the project itself, but none of the individually priced files. This should includes discounts (either on bundles or the game itself).
Individually priced files can only be priced higher than the base project itself, so users can only gain access to them specifically by paying more for the project itself.
This does neither confirm nor deny any possible scenario in regard to those. Includes discounts. How.
Let's use a simple scenario for starters. A single game with discount 50%, price 5, individual priced file at 10. I can pay half, 2.5, to gain access to the project. That much is understandable, since the minimum price is lowered to be 2.5. No questions asked.
But I buy at a discount. As a customer I would expect the whole project to be on discount, including any extra files. So I would assume to have access to the file at 10 by paying 5 at a discount.
Another simple scenario. Two games in a bundle. No discounts. Both games cost 5 and both have an extra file at 10. The bundle costs 10, since there are no discounts. A customer paid 10, so the paid price might be 10 when comparing the paid price against the unlock price of the file. But buying both games outside of the bundle would not give access to either of the extra file, since you would have only paid 5 each. Which would result in a discount that only applies to the extra files, if the paid price of the bundle is applied to each game.
I think the faq should explain how these things work together on the bundle, discount and individual price pages. It currently does not.