Actually, just after writing my post, I restarted yunohost once more and it started to work. the last thing I did was to go into the filesystem and not that /etc/ssl/certs/yunohost_crt.pem points to /etc/yunohost/certs/MY_DOMAIN (MY_DOMAIN being my domainú) and can be read only by root. I changed permissions on parent directories so that they could be read and executed (entered) and changed the permission on the file itself so that it could be read and now it works.
Should all that be unreadable? Keys are secret, but certificates are meant to be public, no?
Edit: but maybe that has nothing to do with that and I just have not refreshed in my browser enough, not sure now.
Edit2: Hm maybe I was wrong and it did not work. Immediately after, I stumbled into 502 error ( WIKIjs and gateway error 502 ) so I reinstalled the wiki. Now no matter what I do, I cannt make this to work, it is always stuck at that error about the token.