I had a problem similar to this and did not like the containers being binded to gluetun (problematic on docker daemon restarts, gluetun container being recreated, etc)
My solution was changing the gateway of each container to be routed through the tun. So first by having them both on the same internal network, then changing the entrypoint of the container I want tunneled to include the gateway change.
For example my entrypoint would be:
... && route del default && route add default gateway $GATEWAY_IP eth0
The container may be missing packages related to route so it may be necessary to modify the Dockerfile to install extra packages.
The reason the gateway must be set at the entrypoint is because docker overrides the gateway to correspond with the networking defined during container creation. And the entrypoint is the last thing executed before the container starts for realsies.
However gluetun also needs to work as a gateway which is done by modifying it's iptables post-up rules file (at /iptables/post-rules.txt). I appended at the beginning of the file the following rules:
iptables -A FORWARD -i eth0 -o tun0 -s 172.84.0.0/24 -d 0.0.0.0/0 -j ACCEPT iptables -A FORWARD -i eth0 -o tun0 -m state --state RELATED,ESTABLISHED -j ACCEPT iptables -A FORWARD -i tun0 -o eth0 -m state --state RELATED,ESTABLISHED -j ACCEPT
What this does is accept any traffic from the net I have my gluetun and other container in, then forwards outgoing traffic to eth0 from tun0, and vice versa for incoming.
Sorry for wall of text this is not very straight forward :(
Can't you use a wildcard SSL cert for subdomains? (*.mydomain.com)