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If you're on Windows, just use win-acme, it can automatically detect IIS configuration and handle Apache, both without stopping the server.
Note that since you're on windows anyway you could also get certs on windows (using https://certifytheweb.com etc) then copy then to WSL (you would add a Deploy to Generic Server task to export the certs as pem files etc and this could write out to the \\WSL$ share path).