(maint) Adjust new environment tests to work with PE

The changes to these tests are in two main categories:

1) Changes to file owner and group to use beaker host references so that
correct user/group settings are obtained regardless of whether a FOSS or
PE run is being performed.  Also changes to permissions to be more
permissive for group so that the puppet system user running under
Passenger can access key files.

2) Changes to basemodulepath to ensure that the modules PE master needs
to run under its /opt site module directory are always present.

In addition a few cases had to be exempted on PE altogether, notably
tests which were testing the effect of commandline environment settings.
Since running a PE master with commandline settings would require
modifying it's rack config.ru file, these tests make little sense in
this context.