I've been working to wrap my mind around this. I think there are a few things that we should think about differently and one bug like issue.
First lets look at the potential bug - non-thru features are not shown on the flat pattern. For one thing i've never known them to show through and this is the first instance i've seen someone try it - i'm not suggesting they shouldn't be shown only that they aren't.
Second. The method for forming the large radii is likely what is breaking the arc translation in the flat pattern not simply because they are ellipses. I tested using ellipse cuts or sketch corners without issue.
Fusion is saying the flat pattern isn't flat. Essentially the lower gap is filled but the face is off by 2.892E-04 deg. Minute, but likely the culprit. Should it be so exact in tolerance for angle deviation when creating a flat pattern? maybe?
Now for the part that took so long. I theorize this is failing because of what sheet metal used to be capable of. So I rebuilt the cover using Bend - which i highly suggest you do as well. This results in no issues exporting and one SINGLE flange rather than extrude join to fill gaps. I cannot repair your model because of that so i had to start over.
Bend allows for significantly less fiddling in getting it to work. Also as of the December update - bend now allows you to do multiple bends simultaneously. Here is the wrap using two bends, one with an override and the other the spine in one shot.

Attached is the DXF and the F3D.
Ryan Bales
Fusion 360 Product Support