I understand the issue however I feel like since Game Maker (by default) names all layers the same, I think the "correct" way to handle this would be to create multiple layers with the same name at different layers. (Maybe if this is not possible I would even go as far as to have a prefix or suffix after the layer name (e.g.: _roomname or _depthvalue). This would be far more convenient than to rename all the layers. I feel like it's not "good" game design to access the layers by name anyways. Far more often you want to have different depth values. Who renames their "Instances" layer in every room for different depth?
Thank you for looking into the issue :)