Same problem here. I am able to work around it by losing the PDF export function of Designer and instead using the pdf print option built into OSX via the print dialogue.
However, that loses all the functionality options built into Affinity Designer, such as being able to specify the type of PDF I want to make.
Funnily enough, enabling 'Simulate Overprinting' in the Adobe Acrobat DC print preview dialogue doesn't help me to see the problem. I literally have to physically print it to see if it's going to be a problem.
Not good.
I hope my workaround helps.
Clearwood, for the colour profile tweak, what exactly did you do? In my printer options for my Brother printer the the options are slightly different.
edit:
Another way is to use FLATTEN PDF