This is a serious limitation of the program then. The obvious reason to save in pdf format when required, is to retain the vector shapes. How could I have worked otherwise? I used a vector design purchased as stock, and needed to change the colors. I couldn't just manually change every single polygon (hundreds of them) so I applied a overlap color mode to it. Pretty normal procedure.
But when I have to output the design I need to give the customer a vector, not a raster image.
When saving a file from illustrator as a pdf file, it's a full vector, so why shouldn't Affinity do the same? If this is the way it works, than it simply doesn't work. Any useful tip so I don't have to do the whole job again with AI?