What the government expect is if you submit your application inland, your wife is supposed to stay inCanada while application is process, I've heard some people who have done short trips and they return back (2 weeks), if your wife meet all requirements and eligibility to enter back, there should not be a problem.
However, the other option will be applying outland and she still can visit you back while the application is in process; again if she meets eligibility to enter back to Canada. People say this process is a little bit faster that doing this inland.
In my experience, my wife has been through similar situation, she came from USA, we decided she stay, I included into my private benefits insurance, we also applied for Open Work Permit (if you do this make sure you pay 2 different fees, in total $100 + $155 = $255) and she has staid with me here in Canada with no issues, after 6 month now she is in "Back Ground Check" status, and currently average inLand applicants is 6-7 months; which vary from case to case.
Hope this could help take the better decision on your case.
Good Luck!