Does anyone know what kind of clone-stamp or healing brush featurs Mari/SubstancePainter/3D-Coat have to fix up seams between UV islands on a model textured in DDO?
The clone stamp and healing brush in Mari were written for (almost) exactly this purpose, so yes. One thing to note is that if you're painting in 3D Mari should never produce seams. You can paint on polygon soup if you like and it won't cause any problems.