You can apply outland and give a Canadian address as your mailing address in which case there would be no need to monitor the mail to an overseas address.
After the 36 days when the file goes to Japan, it would take 5-7 months, see
http://www.cic.gc.ca/english/information/times/international/05-fc-spouses.asp#asia and then she would have her PR.
For inland, it's 5-6 months to first stage approval. That means that she could get a work permit and probably qualify to apply for health care depending on province but the actual PR often takes about a year but can actually take longer.
The complications arise when there are questions about your application and an interview is required. For outland, that would mean she has to go to Japan for the interview but would otherwise not delay your processing much. For inland, an interview can be a disaster because it means that there is no first stage approval, no work permit or health care but the file is sent to your local CIC office in your town and sits there until they have time for the interview which depending on their caseload can be up to 3 years. Another downside with inland is that it's not advisable to leave Canada while it's being processed because if for any reason she can't get back into Canada, she loses the application and all the waiting time already put in.