We are hoping for more automated Nginx integration, on the level of our Apache integration (so that certificates can be automatically installed and automatically renewed). Unfortunately this feature is broken right now, although Python developers who are Nginx users are welcome to jump in and try to help us fix it!
As @Sava says, if you are willing to take responsibility for installing the cert and for renewing it when it expires, you can indeed use the client now to get certificates that will work perfectly in Nginx (and other web servers). One thing to know is that the file
fullchain.pem has the combined certificate and chain, which is what Nginx wants.