I would pack out the studs before installing the Duroc so it goes over the flange on a straight plane. This could be done with something as simple as strips of Modified Bitumen or 90 lb. Roofing material. You should always create a shingled condition when it comes to water, and always give water somewhere to go. Water is the universal solvent. Expecting sealant or Thinset to last forever is a pipe dream.
" A lot of men build things, and a lot of things fall down "