Certbot is no longer being developed for Windows. It was briefly being tried out, but they don't have the effort to continue supporting it.
Also, it very much has a "linuxy" approach to how it does things. It uses symbolic links, it assumes that servers will be configured by pointing to the pem files, etc. Windows-native software usually expects certificates to be in the OS's certificate store and managed as separate things, not really as files. If you were running Apache on Windows, say, it'd be alright, but if you're trying to use .NET and IIS and such it's going to be working against you.
If you need to use certbot, then I think you'd want to write a deploy-hook that copies the files from the live folder to some other place, and have your server software point at that place, if the software can't use the symbolic links directly for some reason (which seems odd to me too).
But you're probably much better off using win-acme or Certify the Web, which are written specifically for Windows and how Windows servers want to integrate with their certificates.