The primary purpose of the test should be to try and identify the heart rate that corresponds with your aerobic threshold and perhaps also your anaerobic threshold. If you usually run on flat and do the test on an incline, there will probably be some differences in your efficiency (running economy), but I don’t think that should be a very large factor. I’d suggest that you focus on having a slow, easy, lengthy warmup (20-30 minutes from walking up to a light jog) before the test. Testing stages should be 3-5 minutes.
Running with a weighted pack can be a recipe for injury. It sounds like you might have some ankle / calf issues to try and work on. Do you have enough ankle flexibility? Running or hiking up an incline, if you’re only transmitting force through your toes or the ball of your foot because your heel isn’t touching the ground can be tough on calves.