The WHV is her temporary status - she can remain in Canada and continue working for as long as it's valid. The marriage and the outland PR ap will not adversely affect that. In fact, before her WHV expires, she can submit an
application to change her status to visitor - based on your marriage and the submission of the outland sponsorship application - and as long as you guys provide proof of your marriage, the PR ap and your ability to provide financial support for her, it will likely be approved and she can continue to remain in Canada with you for as long as that temporary status remains valid. Just be sure the extension ap is received by CIC before her WHV expires, and that you track the delivery so you have proof it was received. That gives her "implied status" to remain in Canada legally until they make a decision.
The outland PR ap has no residency requirement - she can be anywhere in the world and still have her outland ap processed through the embassy that represents her home country. So she could leave Canada and it wouldn't affect processing - however, it also doesn't guarantee she'd be able to come back, and she would lose her temporary status by leaving. If you apply inland, though, there
is a residency requirement and if she left Canada and wasn't allowed to come back, the inland ap would be forfeited.