Hi guys!
I bumped into the same problem. I wanted to cut out these small elements from the flower shape to make a ragged outline (subtract1). I tried selecting all elements and clicked subtract. Subtract0 shows the result. Changing this Fill mode thing does not solve anything. Using Divide seems okay, but still you need to delete the items you wanted to cut out. (I know, I can select them at once in the layers panel, but it's still one more step.)
In Illustrator I select all objects and click "Minus front" (=subtract), so the whole operation is just one click. I hope, these kinds of features get better in time. Now I could solve the problem, but it's really time consuming to search for solutions - and it's probably the most frustrating factor.
Of course, I'll be here waiting for developments. These Affinity software already have some lovely features!