Layering stamps on top of each other in same layer

If I want to overlap trees, do I need to have a different layer for all intersecting trees? I have a stamp that is 4x3 pixels wide. If one of those stamps intersects the other it “deletes” the intersection even though the trees themselves are transparent background. I am guessing this has to do with the CSV type export. You can only have one value on a layer, so it “deletes.” Is this logic correct?

A tile cell in a Tile Layer can only contain one tile at a time, regardless of the format used to store it. If you want multiple tiles at a single location, you will need multiple layers.

Depending on your needs, you may be able to avoid having multiple tiles in one cell by putting your larger entities into large tiles, instead of creating them out of multiple small tiles. Large tiles can protrude from their cell but still take up just that one cell.
I’ve written in more detail about this “problem” here: Tiled Tip Sheet

Your tip sheet covers every annoying case not included in the docs. Thank you so much for making that. It should be in the docs 100%. If it is then it should be more obvious!

Thanks! There’s plenty it doesn’t cover either, and there’s an entire second page I’m still working on just for Automapping.

It’s listed prominently on the “Docs” page, the same page from which you reach the official docs and API reference. I think that’s obvious enough xP