I have had countless headaches over the past few months trying to clone the default Python environment in ArcGIS Pro. I finally got a new laptop and thought that a fresh install would allow me to clone my default environment without any issues. To my dismay, the environment failed to clone. Come to find out that the default python folder has Read-Only permissions. Once I removed the read-only permission I was finally able to clone my environment and install Spyder (same for my old laptop).
I even had ESRI technical support remote into my desktop to solve this issue and that permission was not something they knew to look for. So I just want to bring attention to the fact this is an issue when cloning python environments.