CRA accepts that a couple under the same roof can be living separate and apart
The eligibility of an individual for the Canada child tax benefit or the GST/HST credit under s. 122.5 may turn on whether the individual has a “cohabiting spouse or common-law partner,” whose definition turns, in part, on whether they are living “separate and apart.” CRA accepts the family law jurisprudence that they can potentially qualify as living separate and apart even if they are living under the same roof (e.g., pending sale of the house), and cited the criteria in M. v. H,  2 SCR 3 of “shared shelter, sexual and personal behaviour, services rendered between them, social activities and relations, economic support and children, as well as the societal perception of the couple.”
Without hint of self-consciousness, CRA then provided a list of documents that could satisfy an auditor that these criteria are met.
Neal Armstrong. Summary of 2 February 2017 Quebec CPA Individual Taxation Roundtable, Q.1.3, 2016-0674821C6 Tr under s. 122.6 – cohabiting spouse or common-law partner.