Yeah, it's the chain stay length that will be the major factor, especially if your mtb is running on 26" wheels.

There are panniers on the market that feature mounting systems that allow you to swivel the upper hooks a bit, in order to tilt the bag to avoid heel strike. But doing so almost guarantees you run into an 'either/or' situation- you can mount either the panniers or a trunk bag, but not both at once, which kinda defeats the purpose of getting a rack with the lower rail to begin with.