I could always write a script and run a DNR
Do so. I do not think that you can configure OD itself to modify Deployed Files. You can perhaps code a Delivery Adapterto remove CRs for you. In this particular case it is IMO easier to do by DNR - as you've mentioned
I do not believe that OD adds ^Ms to files being transferred - more likely the editing application being used on Windows is doing that and OD is transferring the file as-is.