Another creator tested this here and unfortunately this just seems to be how Itch handles bundles. I've also experienced this when buying bundles, new/future items just are not included if the creator adds more to the bundle.

Are there game stores that do such? Selling a bunch of items and give ability to change the content of that bundle of items at a later date?

One does not need an account to buy on Itch, so they have to create an entity that holds the purchased items together. On Steam if you get a "bundle", you just attach the items to the account, no matter where they came from. There is not even a possibility to change the "bundle". There exists none.

You treat a bundle like a project page, so using a project page would be the way to do what you want. I am not sure though, if you can transform the bundle content and projects in a way to 100% reflect what you intend to do. On the one hand, you seem to want to give access to new content for previous buyers. On the other hand, if you transform one of the projects into a get-all-items-for-a-discount project, you would give access to all the other items to people that only bought that item. But it might be the easiest way. And it would ensure that future updates to the "bundle" would reach previous buyers.

What I do not get, why they even allow to recycle a bundle, including the name of the bundle, without big bold letters to the developer that this will not change what previous buyers bought. And it does get confusing. The buyer will see the old bundle in the purchased section in the library. With links to the purchased items. But it will also have a link Visit bundle page which will point to the current bundle that will have different items.

But if you think about it, if you were able to change the bundle and add items, you could also remove items and thus access after the purchase.