I don’t think there’s any obvious fix … the way Lets Encrypt works rely on your DNS record poiting to the right IP. If that not the case then it can’t work. Though there are alternative “challenges” in LetsEncrypt which allow to deliver a certificate through different methods, e.g. a DNS challenge. But it’s not integrated in YunoHost so it’s up to you to tweak whatever needs to be tweaked to make it work …