Short answer:
There was a mistake with the GOG codes for some D:OS backers, and the Larian Vault download was a quick fix while they sorted that out.
You can contact GOG support to get it on your GOG account. From the GOG DC release topic:
Anyone who backed the Original Sin Kickstarter and claimed his or her copy of Divinity: Dragon Commander on GOG and *didn't* get the Imperial Edition code issued, please contact Support and we will give you a free code for the DLC. In the subject of your ticket, please put, "Imperial Edition Upgrade for Kickstarter Backer".
