UPDATE: I thought the below was correct, but with further testing have found some continuing issues with the Alpha channel bleeding through and modifying the RGB channels using channel packing. I'm still not sure why my first test image worked and the subsequent 9 tests didn't.
I've tried to read through all the posts to see if anyone else has a similar method to what I'm doing. I'm on day 3 (maybe 4) of a trial of Affinity Photo and like many of you use the Alpha Channel to pack more information into a texture, I've also been frustrated by painting on the RGB layers and having the values affected by the Alpha channel.
To get around this, I have a Spare Channel as a "Blank Alpha" and another one as my "Final Alpha". I've also been doing the same with the RGB channels and any variations and references for a material. If I need to make any changes in RGB, I load the Blank Alpha into Pixel Alpha of the layer I'm editing, make the changes and prior to save, load Final Alpha to Pixel Alpha. For export it's pretty much the channel packing video, but from my test I'm selecting from a longer list of spare channels, currently 16.
This allows you to edit other channels independently in grayscale without that weird multiply effect based on the alpha, it also allows you to edit RGB normally (switching Blank Alpha with final and back). It's not perfect, but it may work for you as it is working for me.
Keep in mind I've only tested saving to PNG and importing into UE4, I've seen other people mention TIFF, I have not tested this format. Hope it's useful.
Jamie