How to patch core via drush-make when using a stub make file?
Include the core patch in the core stub makefile. Here is mine straight out of buildkit.

api = 2
core = 7.x

projects[drupal][type] = core
projects[drupal][version] = "7.39"

; Use vocabulary machine name for permissions
; http://drupal.org/node/995156
projects[drupal][patch][995156] = http://drupal.org/files/issues/995156-5_portable_taxonomy_permissions.patch

projects[example][type] = profile
projects[example][download][type] = git
projects[example][download][url] = git@github.com:Laudanum/example.git