@Andreas Meier Thanks for the question. Are you trying to upload data using AML Designer or AML python SDK?. You can upload data using upload_directory API.
The OutputDatasetConfig allows even to register the output as a Dataset, where getting rid of such folder structure makes sense. From the docs itself: "Represent how to copy the output of a run and be promoted as a FileDataset. The OutputFileDatasetConfig allows you to specify how you want a particular local path on the compute target to be uploaded to the specified destination".