Broadly speaking there are two types of store specific bonus content:
Bonus content paid for by the publisher in Japan in order to boost sales (often at the request of a Japanese book store, sort of like a co-op in western retail)
Or
Bonus content paid for by the book store (or affiliate of the book store). Which are done by the stores as part of their marketing and they usually hire the japanese publishers to make it for them.
In scenario 1 the rights to this extra content are usually held by the publisher, the same as the main book. In scenario 2 the bonus content was done as a work for hire scenerio, so the rights would be held by the store. However the bonus content is still derivative of the main work, so licensing it would require approval from the jp publisher in addition to negotiations with the store. Rather, in the cases where we have gotten this content, it's likely the case that the jp publisher buys the rights back from the store, and then resells them to JNC.
Jp publishers have different stances when it comes to this bonus content. Some are happy to provide it (the ones they have rights to) to overseas licensors for use in marketing or sales etc.
Some require additional money.
Some ask for ridiculous amounts of money.
Some are too disorganized and do not even attempt to do the legal legwork to make them available at all.
Some give restrictions for their use which are unrealistic given ebook formats (only can be used as a physical printed bonus, etc).
It's a mess and we do our best.