I usually make a dedicated user for torrent clients. Works well. This allows me to run multiple instances of transmission in the vm, for example. Manage them through systemd services.
Clash sounds interesting. How to manage depends on clash rule options and management features.
By default, most torrent clients will open random outgoing ports on the default interface. For the listen port, it will be opened locally and they will try to open an incoming port with upnp
Probably the most suitable client for this is qbittorrent. You can assign a specific network interface and incoming and outgoing ports.
You could create a virtual network interface just for your client. Tag it with VLAN for easy management by clash.
You could definitely collect the ip addresses of the most common trackers, but it would be impossible to collect the ip addresses of all possible peers.
Sounds amazing. Please share a github/gitlab repo that we can follow and test.