I've always set my TiVos to output a constant resolution, to avoid the flicker that accompanies a mode change. Currently, I have a Premiere set to use only 1080i, and a Roamio set exclusively to 1080p60 (on two different TVs). Yet, sometimes I still see the flicker, on both these units.
It only happens with some network-transferred videos, which cause the flicker just as I start them. The sad thing is that the before and after resolutions are the same -- the TiVo is technically obeying my settings, but still invoking an unnecessary mode change, to switch from one resolution to the same resolution.