You pretty much lost me with the surprising attitude about a simple zip file, which adds a single step to the process and is commonplace. I would have thought the time and effort put into tracking down and describing the issue would have been better received. I've often wished I could improve or extend paint.net but I can see now why that's not a thing.
I'll add the requested file since I did the work to investigate and happen to have the repro, but the only way to attach it is via...Startup.1.zip zip; hopefully that makes sense and is expected.
Finally, the first time Startup.1.profile was generated after renaming/deleting the file and running paint.net and passing a command line argument, the file was large (189kb). However, when I came back later, it had changed and was the same size as the one which previously caused the problem behavior (54kb), yet it still works. I repeated the process and confirmed it changes size likely based on some loaded state. Seemingly expected behavior, just thought it's interesting to note if you're comparing the before/after versions of Startup.1.profile and wondering why I originally said it was 190kb but it's small in the zip. Also, Startup.1.profile_bad in the zip file is the repro case which prevents command line behavior from working correctly, the others are currently working versions.