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This question was answered by @ryanpq:
It sounds like the soffice process being used in the background for document conversion is the thing that is encountering permission issues for you. It is possible to start the soffice process in a headless state as a non-root user but appears to require some workarounds. This forum thread provides some more details on getting soffice running headless as a non-root user and once soffice is running as the same user as your web server the permission issue should be resolved.