Do you mean the Win+Ctrl+D shortcut?
Yes, this is a real limitation. Windows currently has no built-in way to disable Ctrl + Win + D individually. PowerToys or another remapping tool is required.
You are posting in public community forum. As much as I would like to help you, I can only provide you with the information, but it is out of my control to change the product.
I would suggest that you submit a feedback via Feedback Hub (Win+F), that way it gets to the product team and they do gather data from there. They just don't gather feedback from here.