Pacman 5 calls its hooks in alphabetical order. The hooks I added in my previous patch (see [Patch] Support Pacman 5.x hooks) have no numerical prefix -- which is needed in order to ensure that Pacman calls the hooks as late as possible (i. e. after all other hooks).
My patch remedies that minor issue by adding the proper numerical prefix to the filenames of the Pacman 5 hooks. It may be found here: https://github.com/Tblue/etckeeper/commit/33b2d1edb9dac1ad04cf8ab100b8edff0b004dd1.patch