It depend on how they want to make the deal.

Your sample case, the local manga licensee already published titles from Kodansha, so they have the channel to license stuffs from that publisher.

Well, in the end, Type Moon as the author could refuse licensing the title out (for example, there are author who refuse because personal reasons like they don’t want the art to be censored, or they think it’s too sensitive for foreigners). But most of the time, if author is publishing through a publishing company, they usually trust the company to deal with most of the business side, including licensing, with them only interfering if they really think it’s needed.

Kara no Kyoukai are also Kodansha, like Monogatari series, although the manga version is Seikaisha (which if I’m not mistaken is Kodansha’s fully owned company, like Ichijinsha who used to publish ˜˜Carnival Phantasm Prototype˜˜ Take Moon).