Is ipv6 enable on your server ?
Could you return the result of a “ping6 wikipedia.org” ?
My theory is your dnsmasq timeout due to a broken ipv6 (or broken ipv4 o_O) configuration. If ipv6 is enable, but you are not able to ping correctly outside, IPv6 DNS could be unreachable and it might cause the failure of dnsmasq “timeout”.
So the idea to check that could be to diagnose your nude VPS connectivity (without yunohost installed), by running ping wikipedia.org and ping6 wikipedia.org