When creating the workspace template, the wiki macros are not correctly registered. This makes all the workspaces that are later on created using the template to also have unregistered macros.
This is caused by the fact that the default XE xar used as base template has specified as author "XWiki.Admin" for the wiki macros, but the local admin in a workspace does not exist. This causes the macros to not have enough privileges and not be able to register.
A simple workaround is to resave the problematic WikiMacro documents with a user that has admin rights in the problematic workspaces and also in the workspace template.