The general recommendation is to make a new installation separately from the Steam release. You can remove it or keep it - your choice, it is not involved in the installation in any way. The Steam release is this mod preinstalled on Skyrim SE, so you will be installing it on Skyrim SE by yourself as well.
Your steps are: - Install Skyrim SE - Run the web installer
Your steps are:
- Install Skyrim SE
- Run the web installer