Hi there,
It looks like installing Yunohost on a subdomain (by default) comes with few troubles… I’ll try to investigate further way, but if anyone had already run into this issue, you’re welcome. 
Firstly, I’ve successfully installed Yunohost (2.4 upgraded to 2.5) on a VPS.
The main domain has been configured with a subdomain (i.e. cloud.mydomain.tld) at installation (see DNS zone below).
Then, Nextcloud has been installed successfully and set as the default app (i.e. https://cloud.mydomain.tld redirects to https://cloud.mydomain.tld/nextcloud).
So far, everything’s worked fine, but…
I’m unable to connect my XMPP client to the server.
Metronome’s logs show:
Feb 17 06:48:00 certmanager error SSL/TLS: Failed to load '/etc/yunohost/certs/mydomain.tld/key.pem': Check that the path is correct, and the file exists. (for mydomain.tld)
Feb 17 06:48:00 certmanager error SSL/TLS: Failed to load '/etc/yunohost/certs/mydomain.tld/key.pem': Previous error (see logs), or other system error. (for mydomain.tld)
It’s like Metronome was set with the root domain (which isn’t assigned to this server). I tried to symlink mydomain.tld to cloud.mydomain.tld: metronome started without throwing any error, but I’m still unable to establish a connection.
Here is the DNS zone I use:
;; MX Records
cloud.mydomain.tld. 300 IN MX 10 cloud.mydomain.tld.
;; TXT Records
mail._domainkey.cloud.mydomain.tld. 300 IN TXT "v=DKIM1\; k=rsa\; p=xxxxxxxxxx"
cloud.mydomain.tld. 300 IN TXT "v=spf1 a mx ip4:xxx.xxx.xxx.xxx ~all"
_dmarc.cloud.mydomain.tld. 300 IN TXT "v=DMARC1\; p=none"
;; SRV Records (Service locator)
_xmpp-server._tcp.cloud.mydomain.tld. 300 IN SRV 0 5 5269 cloud.mydomain.tld.
_xmpp-client._tcp.cloud.mydomain.tld. 300 IN SRV 0 5 5222 cloud.mydomain.tld.
;; CNAME Records
muc.cloud.mydomain.tld. 300 IN CNAME cloud.mydomain.tld.
pubsub.cloud.mydomain.tld. 300 IN CNAME cloud.mydomain.tld.
vjud.cloud.mydomain.tld. 300 IN CNAME cloud.mydomain.tld.
;; A Records (IPv4 addresses)
cloud.mydomain.tld. 300 IN A xxx.xxx.xxx.xxx