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Yes - review this article https://www.linkedin.com/pulse/lets-encrypt-part-2-3-repurposing-clients-making-things-andrei-hawke
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You don't have to do anything - however there are easy ways of doing things and hard ways. Review the article above.
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I would recommend not using the CSRs from microsoft as they tend to have a whole of extra fields and properties which are specific for microsoft.
Shame there's not a semi-automated way to do this with letsencrypt.org, much like I'd been doing with Godaddy (show I control the site with DNS or by putting a file on the web site, submit the CSR, get back a cert with any intermediate certs, install them. Not very complicated actually. I wouldn't mind doing that every 3 months until I moved to 2016?
That is exactly how some of the clients work.
Review these clients:
Andrei