Upfiring speakers behave differently than ceiling speakers in Dirac Live (if they have been properly labeled in the device).
The speaker type should be "DOLBY_ATMOS_SPEAKER" for upfiring speakers. This should trigger a pre-emphasis filter being applied on the device to the stimuli played through such a speaker.
The pre-emphasis filter is there to ensure that the special Dolby-patented target curve for such speakers is not "destroyed" by the Dirac Live filter design.
Basically, the pre-emphasis filter will hide the Dolby-filter from our measurements. This doesn't happen in Dirac Live, it happens on the device.