One of the options for primarily keyboard users would be to have the add layer button tabbable just like you can select a layer.
To add keybinds that run the same command, I would duplicate it with a dropdown menu (...) and then handle removing empty and duplicate entries. This is better than allowing two keybinds to call the exact same command because you can set up different conditions. That said, the conditional should be copied when the keybind is copied.
Keybinds could be filtered by conditions. These conditions should exclusively be identifiers (maybe nested with dot-selectors) and potentially negated with (! or NOT). If I add &&/AND and ||/OR, I will require parenthesis around every pair (in that case, all conditionals would implicitly be surrounded with parenthesis).
Layer settings should be able to reference settings from other sources in their list where it makes sense. This basically breaks it up into a list of which settings are listed and where to find them, and how to display this layer's settings. The reason referencing external settings is useful is because some settings should be global/external from a organization stand-point, but still be modifiable from a local thinking mind-set. In any case, I should restrict settings to be shallow (1 layer deep) and require that settings sources have an icon (e.g., NumberLayer has a number icon, SelectionLayer has a selection, global settings have the text GLOBAL). I think I want to have the layer icon for other reasons anyways.