Yes, we have a tracker issue regarding this problems. Custom keymaps does not natively work with Mac oskeys. And they have some more flaws. We work at it. But haven’t found a way to fix this yet. The whole keymap code is crazy implemented. Even the Blender devs are in trouble to change things there.
As a workaround, you can for now use the Mac keymap that we have added. It has the oskey mapped instead of ctrl. And then undo should work. Simply change the keymap to Bforartists-macOS in the keymap manager.
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