Well diagnosed. The problem arises when the user directory is a subdirectory of the default. In fact that is not a good idea. I think npm will look in directories above the current one when loading modules, so putting flows in a subdirectory of the default is not a good idea, it could cause confusion. Therefore, I suggest using your first example, keeping the folders separate.
I am not sure whether this is a bug in the node-red command or not.
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