Patch a module loaded by a distribution
For now I have solved this by patching the make file of the commerce kickstart profile:

projects[commerce_kickstart][type] = profile

projects[commerce_kickstart][patch][] = patches/commerce_kickstart.patch


The content of patches/commerce_kickstart.patch is this:

diff --git a/drupal-org.make b/drupal-org.make
index bde036e..787f6ea 100755
--- a/drupal-org.make
+++ b/drupal-org.make
@@ -31,6 +31,7 @@
 projects[taxonomy_menu][subdir] = "contrib"
 projects[libraries][version] = 2.1
 projects[libraries][subdir] = "contrib"
+projects[libraries][patch][] = patches/libraries-from-inherited-profiles.patch
 projects[views_megarow][version] = 1.0
 projects[views_megarow][subdir] = "contrib"


The patch happes to be applied on the commerce kickstart before its own makefile is executed. When it finally get executed it will also applied my libraries module patch within its directory structure.