It's OK to have unshared application caches (directories or memcached) BUT (and this is a big butt), you (as a sysadmin) need to MANUALLY CLEAR THE CACHES at the right times (for example, every time you upgrade Moodle code).
There is unfortunately no tuning guide for this in our docs, but I am asking our developers to fill this out: http://docs.moodle.org/25/en/Caching#Cache_definition_configuration (MDL-41067)
I'd appreciate help from anyone willing to look at the MUC-related code to fill out details in those docs.