When your spouse moved to Canada, you should have inform the change of Country of Residence. If you have not so, then you should do it. When you receive a PPR, your will have to land first and become a PR, before your spouse can be issued a COPR. Your spouse will not need to send the passport as she is in Canada and only needs a COPR and not a PR visa.
As regards the PR, IRCC is continuing to send COPRs to inland applicants on regular basis. Given that you have a PR application in process, and that your spouse in currently in Canada, during the final review a Field Operations Support System (FOSS) check is done to determine your current immigration status in Canada for all individuals in the application. During this it will be clear that your spouse is a TR in Canada.
However, you should inform IRCC of the change of CoR if not done so for your suppose.