TL; DR: Is it possible (and if so, desirable) to configure my OPNsense router to handle non-standard traffic instead of needing to configure each client device manually? Examples of what I mean by ‘non-standard traffic’ include Handshake, I2P, ZeroNet, and Tor.
You mean run those programs directly on opnsense? I don’t believe there is any way to do that.
No configuration is needed on opnsense to use them as normal on your devices though, so that’s your best option.