I've seen a number of discussions, but somehow they never really "solved" it, as it seems. The problem I experience is that when using a PMS color as a SPOT and OVERPRINT color in a separate layer, the export fails to retain this. Not only is the layer renamed, but also the PMS color (the actual PMS, not the layer) is lost. When importing the pdf, the PMS color (layer) is converted based on CMYK. This happens both in Photo and Designer.
What did I do? I've added the color (PMS 803 U) as a Global color, with SPOT and OVERPRINT selected. I have selected the item, filled it using the bucket and then renamed the layer. I've saved it using Export >> PDF >> Preset PDF/X-3:2003. Here I kept everything standard, including: overprint black and honour spot colours. Then, when testing, I see that the two layers are there, but the PMS color seems to have been changed.
The printer says this isn't possible with Affinity, but I hope it is. Would hate to have to go back to Adobe... Any help is highly appreciated!!