I have encountered this same problem. I have a spot color design using 2 Pantone inks. When I use "separations preview" it looks fine. When I go to "print" and "output", only the 2 spot colors should have a small printer icon next to them, but the CMYK also have the small printer icon next to them. If I remove the freeform gradients from the file, the "print" "output" is fine.
I have encountered this same problem. I have a spot color design using 2 Pantone inks. When I use "separations preview" it looks fine. When I go to "print" and "output", only the 2 spot colors should have a small printer icon next to them, but the CMYK also have the small printer icon next to them. If I remove the freeform gradients from the file, the "print" "output" is fine.