Make add layer a list of checkmarks so you only have one at a time?
I need to ask the question: What were the reasons for adding duplicate layers in the first place?
Users want to be able to draw certain elements of a layer above or below other elements
First off, this is an uncommon feature-need. Second, this can be done using separated groups like how answers and questions are grouped separately.
certain layers prevent overlap, like you can only have one number per cell, but sometimes that needs to be overridden to allow zero or one number per answer question group (so, two numbers max). This is especially true if I only have one number layer that can render to large and small numbers but they need to be able to overlap still.
This basically comes down to allowing intra-layer interactions (layer interactions with itself). This is also a complex requirement. It also runs into the "all things visible" guide. intra-layer interactions should not discriminate between two objects of the layer for no reason; there must be a differing visual or 'physical' attribute between the objects that differentiates their behavior.
While it's not duplication per se, I did see a possibility of having layers be composable and that's a reason to have multiple of the same type.
But at that point, it's duplicate behaviors not duplicate layers/tools.