Within a conemu-inside control, run FAR (the globally installed instance).
If there's a per-machine ConEmu installed which has been integrated with FAR, then FAR would attempt to load its ConEmu hook plugins from the globally-installed ConEmu instance, which would not match the version of ConEmu running in the inside control. As they're probably not binary compatible, there would be errors.
Within a conemu-inside control, run FAR (the globally installed instance). If there's a per-machine ConEmu installed which has been integrated with FAR, then FAR would attempt to load its ConEmu hook plugins from the globally-installed ConEmu instance, which would not match the version of ConEmu running in the inside control. As they're probably not binary compatible, there would be errors.