This is a very strong explanation of what’s going on. And as a follow-up, I believe that ZeroTier present a single Ethernet broadcast domain, and so WoL tricks are more likely to work naturally there than with Wireguard. I haven’t used ZeroTier, and I do use Wireguard via Tailscale/Headscale. I’ve never missed the Ethernet features of ZeroTier and they CAN result in a very chatty wan if you’re not careful. But I think ZT would make this straightforward.
Though as other people note… the simplest/least-disruptive change is probably to expose some scripty thing on the rpi that can be triggered via be triggered over a routed protocol and then have the rpi emit the Ethernet broadcast packets from the physical network.