affinity publisher is just the worst offender when it comes to placed pdf documents. i would recommend, if possible, converting all pdfs to eps documents or us the action "convert all fonts to outline" in acrobat pro and then place those pdfs as interpreted.
passthrough is just not working with any pdf besides publishers own. specially adobe pdf exports don't work in publisher.
just outline fonts in acrobat and then interpret the placed pdf is the best option, highly recommended, all colors as expected, no errors.
downside, you will need to purchase a full license for acrobat pro