They shouldn’t have been, this seems like a bug. I have a vague recollection of hitting something similar in the past months and fixing it, are you on latest mne-bids-pipeline main? If not, can you try it to see if this is fixed?
Typically whatever processing you apply to your task/rest data, you apply as similarly as possible to your empty room data. That way if you compute an empty room covariance or anything from it, the task/rest and empty room data remain comparable.