Hi John,
I've been traveling and had not had access to Affinity until now. Let me try to explain more clearly.
I have a iPad 2. Totally useless for this project.
1. When I try to create an Affinity stack on my desktop I can indeed see the component layers. However, not all the information I have provided is shown. Affinity has cropped my image so that I have lost part of the information. In this example it is the stem of the flower that is missing as you can see below.
2. If I produce a panorama, Affinity gives me access to the full range of the files that I provided including the flower stem in this example, but, because of the nature of what I am trying to do, they are stacked on top of each other so that I cannot see the underlying info unless I click through them. There is no layers panel available.
3. Trying a Focus merge, the layers panel is available but only shows one pixel layer without access to the underlying layers. Because I am shooting moving objects since I often have to photograph in windy conditions (our last location was on a mountain top at 9300 feet), the resulting image has way too many ghosts which make it impossible to work with.
What I've been doing up to now is using the Photoshop Photomerge and simply unchecking the Blend Images together option. This produces individual layers which are aligned but are fully available for me to mask as needed.