I was a bit daunted by this problem as well. Once I learned how to use artboards the final cropping problem disappears. Using the artboard tool you can resize the complete image, with all layers and edits intact, to the exact right size. Then export the artboard in the export persona. Using the artboard tool you can quickly trim off unwanted transparent areas.
You can do the same thing by going to the export persona and use the slice tool to tell affinity photo what part of the doc to export as a slice.
Affinity Designer has taken some getting used to, but i am really enjoying it. With artboards and slices you can have many sizes and versions of a file in one document, and control exactly what you wish to export.
