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Yes, you can set those variables by exporting custom facts to the environment in which puppet apply executes, e.g.:

[root@puppet glarkin]# facter -p | grep ^basedir
[root@puppet glarkin]# env FACTER_basedir=/tmp facter -p | grep ^basedir
basedir => /tmp

You can add the appropriate FACTER_basedir and FACTER_logdir environment variables, and puppet apply will pick them up from facter when it runs.