If your work permit request is denied while flag-poling, you can still enter Canada on a valid visa that you have. You will be on your visitor status still.
However, one thing to keep in mind is that every time you enter Canada, a CBSA (border) officer makes the decision to let you in or not. Having the visa or the eTA does not mean you'll be automatically let in. That being said it is very rare for an officer to refuse entry to someone who has a valid visa and this only happens under extreme circumstances. So basically, you should be fine.
