OK, I’ve figured it out:
The Augeas parser doesn’t like indented comments at the end of the configuration file…
For example, this is fine (for clarity, I left out the top most of the file):
(...)
</VirtualHost>
#Foo
An extra blank line doesn’t matter, this is also fine:
(...)
</VirtualHost>
#Foo
However, when you try adding spaces or tabs, it doesn’t like that! These configuration files return the error!
(...)
</VirtualHost>
#Foo
(Notice the subtle space before the comment.)
(...)
</VirtualHost>
#Foo
Not good too!
So: remove the trailing comments (not required anyway) and you’re good to go!