Thinking more about this, I don't think this really makes sense or 
gets us anywhere. You cannot force PEAR to only use a single 
configuration file, it always uses both the system and user 
configuration.
The reason to re-consider the configuration storage for horde_role was 
to avoid people getting confused (or confusing their PEAR install) if 
using different users (and thus different user configurations) with 
PEAR. Storing horde_dir in the system configuration would help with 
that, because it made the horde_dir configuration available to everyone.
OTOH the user configuration takes precedence over the system 
configuration, which means it's possible to have different horde_dir 
configurations in the user and system configuration which would 
probably cause even more havoc. Better let PEAR installation fail 
because horde_dir isn't set, than having it succeed but installing 
into an incorrect directory.
There might be more pros and cons, but for now this seems too risky to change.

Still on my todo list to look at before the RC though.

Don't think this needs to be considered a show stopper.

Test setting the system configuration instead of the user 
configuration when setting the horde_dir variable in Horde_Role.