When your subject matter varies considerably in altitude, there are a couple of things you should be thinking about:
If you take off at the bottom of a deep quarry or hill, it's possible that the landscape around you may be higher than the height your drone is flying.
Equally, if you take off from the rim, your subject is going to be made of fewer pixels and so a lower resolution (higher ground sampling distance) in the final orthorectified image.
Stitching maps with high-quality elevation generally requires at least 7 images of each point on the ground. As you'll see in the diagram below, it's easy to drop below this with just a small change in elevation.
When flying from the base of hilly terrain, or terrain with tall buildings, trees or stockpiles, we recommend you create a number of overlapping flight plans, with takeoff points at each plateau. An alternative is just to increase your takeoff overlap to compensate.
We have released an app to help people flying over hilly terrain. Try our overlap optimizer