You shouldnt have to. What version of MD are you using, what are your steps. I will try to run my workflow from memory in case you missed anything.
1: Model, and upload character to Mixamo.
2: Download T pose and animation fbx from Mixamo.
3: construct the animation with T pose on frame 1using motion clips.
4: take note of project, and render frame rates to make sure they match.
5: export fbx animation from C4D. Import it back to make sure its playing the same as the one still in scene it was exported from.
6:Import into MD, make clothes. If the model in C4D is going to have a SDS tag on it apply smooth to model in MD, feature not in older versions.
7: check frame rate in MD that it matches C4Ds. Simulate cloth, export cloth as Alembic.
8: Import cloth back into C4D, it should play fine with no intersections.
PS: also worth mentioning that you can add skin thickness in MD so its not too close to skin. What can also cause issues is if your model is smooth in MD and not in C4D or vice versa. Iv just gone through a project from beginning to end in R21, Mixamo, and MD 8 and had no issues with intersections.