I'm using 4.2.d and have this issue. If I want to embed an image into the wiki and I go to the Insert Gallery Image. It gives images for all Documents (and pictures) from the Document Library within that site. Is there a way to specify only a certain folder within that document library?
It must be using filepicker which you can configure and add control parameters though which you will be able to achieve your goal. You need to figure out which form config gets invoked during that wiki creation and override that with the field which is having file picker associated with it. Not sent percent sure about this code can be in js file as well.