I've tried it with symbols and it's just that creating a symbol for each object is additional work, and selecting gets slightly difficult.
I believe what happens is, I'm able to select symbols individually, and I'm able to select the original shape for the symbols, too. When the shape is indicated (blue Affinity line that follows the shape exactly vs. blue bounding box) then the original shape is selected.
When a symbol is selected, I can make a transformation/translation by moving it, which is not what I want.
So all I need to do is a bit of extra work for setup + not translating one of the symbols accidentally.
Edit: I think it's extra work per shape, because it's (really) not currently applicable on groups, so that "bit" of extra work is actually too much. Although, it's the only automatic solution later. Hm. But still, just too much extra work.
_____
What Affinity does in this case seems to be default behavior among a few drawing apps, somehow? Paint.net does a similar thing, which I recently noticed. In terms of layer operations, kind of, it interprets empty areas as having full opacity. And it appears, someone even made a plugin that makes empty areas being interpreted as having no opacity instead.
I don't know about the work of the developers, but keeping up the selecting system in Affinity is probably much more than just adding some boolean operation, I guess. I'll patiently wait, for any convenience feature. I'm not really dependent on these, I hope. Better not.