For an example of how to use the VPN only for programs that you bind to the VPN IP address see this: https://github.com/tool-maker/VPN_just_for_torrents/wiki/Running-OpenVPN-on-Linux-without-VPN-as-Default-Gateway
or https://gitlab.com/tool-maker/vpn_guides/-/wikis/Running-OpenVPN-on-Linux-without-VPN-as-Default-Gateway
That example does not use Eddie. But you should be able to adapt the exit code there for use with Eddie. It sets up "source address routing" for the VPN IP address. And creates the illusion that the local IP address is the same for any server. You can then bind rtorrent to that local IP address ("bind = 10.44.0.2" in rtorrent.conf).
If you would be OK with having the VPN be the default gateway, just so long as you can still access your remote server by ssh or nginx, then see this: https://github.com/tool-maker/VPN_just_for_torrents/wiki/Maintaining-SSH-Access-Using-a-VPN-on-a-Remote-Linux-Server
or https://gitlab.com/tool-maker/vpn_guides/-/wikis/Maintaining-SSH-Access-Using-a-VPN-on-a-Remote-Linux-Server
When the VPN becomes the default gateway, access to ssh or nginx from remote locations will no longer work, unless you do some set up before starting the VPN, as in that example.
The examples use iptables. I have been meaning to update them to use nft, since iptables will be deprecated before long.