Here's the second part to this design issue and why it needs to be built. Because PMW keeps those downloads in the library, and my auto-import settings analyze audio and update tags, it will scan these files and change them from the original downloads. While not "harmful" per se, it's not what I want the software to do. I want it to ignore my download library so that it's pristine and only act on the location that I told it to import from.
This is definitely a wish list item to be able to clearly configure. I think this is as "simple" as adding an "add to library" option to the Pono Music service so that we can de-select this option. If it's not added to the library, I don't think PMW will muck with the files. The other option is to ensure that the auto-import functions ONLY acts upon files in the location that you specify for the import. Either way, this should be low hanging fruit to put into a new release and ease some frustration.