I am currently working with affinity photo 1.10.5 on windows 10 and I also have this issue. The strange thing is that sometimes it works fine. I take two layers with hard pixel edges and when merging the pixels stay as they should be. But sometimes I have a layer which cannot be merged with another layer (or be rasterized) without the edges being anti aliased. I have no idea what the difference is with other layers I make that don't have this issue. Attached the file with the problematic layer. The layer with the horse on it. Also a little video clip of rasterizing and merging the files to illustrate the problem https://streamable.com/0zdf2c
merge-problem.afphoto