Calling such a concept a 'layer' is quite confusing, given my experience with Photoshop, OmniGraffle, Pixelmator, and most other drawing tools I've seen. Why not just call it an "element" or "shape" or "item"?
In Photoshop a layer could have many shapes on it, if you drew one shape/mark on top of another within one layer, they would be inseparable. If you drew any two things in Sketch, they would always be separate, I suspect this is why they stuck with the term "Layer" even though something like "Object" may have been more accurate.
In sketch, instead of sheets of paper that match the size of the document, you have a perfectly cutout shape for each stroke you draw. You can then move that cutout around within the document.
Both of those have the same principle except one is cutout one is not.
When each layer is a transparent sheet it has an absolute Z order that translates 1-1 with the physical thing it’s virtualizing (transparencies, probably from traditional animation).
However if you cut out tiny shapes and arrange them with some on top of others to make a larger composition, there is no longer an absolute Z order to any element because there are a bunch of smaller stacks of various heights.
The virtualization no longer translates to the physical world, and from my experience that disconnect can sour people against a new way of doing things, regardless of whether it’s better.