@mluessi I can remember that having ref_meg=True caused a series of bugs with my 4D data that come with ref channels but without comps. Problems were ranging from averaging over ICA to viz ...
This is a reason why I pushed defaulting it to False a few months ago.
I think having refs downstream (Epochs, EvokeD) could work if we would make sure that those channels are always ignored internally e.g. treated as non-data channels.