You are correct. It would erode the authority of the deputy heads to administer their organizations and potentially erode the authority of the minister to issue directions to both of those agencies.
The minister, of course, is now the only person who can issue a directive to the deputy head, to the commissioner of the RCMP or to the president of CBSA. Adding another person into that mix with directive or order-making powers complicates that accountability relationship and erodes the obligation of the deputy heads to answer to the minister, who in turn answers here.