If you mention on a visit visa application that she is not planning on returning to her homeland, the visit visa will likely be refused.
An outland application doesn't mean that she can't stay in Canada. On the CIC website, it says that applications from Japan are processed in Tokyo but there is no timeline on the CIC website for Tokyo. Another guy with a Japanese spouse said they had asked and been told that applications go through Manila. If that is true, according to
http://www.cic.gc.ca/english/information/times/international/05-fc-spouses.asp#asia it would take 4-7 months plus one month in Mississauga at the start for sponsor approval so 5-8 months to get PR. She would only have to leave Canada if she is called for an interview.
With inland, 6-7 months for work permit but 10 months to 2 years total for PR. It is really not advised to travel while doing inland. If you would leave and she gets refused entry to Canada when trying to come back, she would have to go back to Japan and you'd have to apply again outland.