If you apply Inland, she must stay in Canada during the entire process or her application can be forfeit. If you apply Outland, she can travel, stay in Canada, or stay in the USA (as long as visitor visa rules are respected, its default 6 mos when you enter Canada or the USA, as a Canadian or American. Do not overstay!).
When I applied during the Harper admin, Inland applications took 3+ years and Outland took 8 months, so most of us opted towards the latter - work permits be damned. However, that is not the case anymore. I believe the application wait times are much more equivalent now!
If she at all wants to stay in the USA or visit the USA during the process, you would need to apply Outland.
What country is her passport from? You mentioned she is a US PR. Keep in mind I believe the country-specific application requirements are specific to her citizenship.