I found an overprint bug in Affinity Designer 1.6.1 (from App store).
1. EPS logo dropped into sign
2. export or using slices with "Overprint Black" checked will actually set all colors to overprint, even when the colors are not set to overprint in the original file. There is rarely a case that anything should overprint other than black.
3. This only happens with EPS files. As you can see in the screenshot from Acrobat that the PDF to the right did not overprint but is correct.
Unchecking the box "Overprint Black" in the More dialog box will enable it to not overprint all the other colors but that is just a workaround and could cause other problems.