Hey,
i’m not sure but i think this looks more like a question for an nginx support forums (i think this could be the reason why no ownCloud user was able to answer this yet 
).
From what i know ownCloud also requires a special nginx config (i had preserved it in Nginx documentation (Unofficial (Community) ) before it was removed by the ownCloud people from their documentation) so it could be also possible that you can’t use certbot to create the nginx config at all.