You can apply outland if you want to even though you are on a study permit. If you apply inland, it would be safer for you not to travel. However, if you leave Canada with a valid multiple entry visit visa and a study permit, it's very unlikely that you would be denied entry coming back. The biggest risk is for people who don't have a multiple entry TRV. If such a person left Canada and then applied for a TRV at a Canadian embassy overseas, immigration would very likely deny based on that their plan is to stay permanently and not to visit.
You should keep your study permit separate from your PR application. Apply for a study permit renewal normally as you would otherwise have done.