Thanks everyone. I did some experiments, and I think that I understand now.
What I found: when I check the "live alignment" option in the "new stack" window, Affinity Photo adds a perspective filter to each image.
When reviewing alignment, I uncheck all the images but two, and set the blending mode from "Median" to "Range" so i can see the difference of those image.
I use an image as a reference, and move the others.
Then, for each image, I first use the Move tool to move the image, so the center of the image "disappears", and then double click on the Perspective Filter to change it, dragging the corners until everything disappears (if they are perfectly aligned, the resulting stack in "Range" mode is almost black).
Unfortunately, when stacking photos taken with wide angle lenses translations and rotations aren't enough to align images, since lenses could cause several complex distortions.
But I found that using the Perspective Filter I can almost always get a perfect alignment of the images. Awesome!
