Hi,
popped out tiles should be easy to delete. They should be selected after popping up. (so you need to just press Delete)
OR
you can hold ALT when dropping script tile to already occupied slot. It should replace the one underneath.
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I think you (and I am sure I would) would hate it. You would delete your tiles while editing them by mistake. -> However, behavior change 1.10 - 1.11 is there by mistake. We will think how to improve it.