Selfhosted
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WoL works as Ethernet¹ broadcast, while Wireguard routes IP, one level above that. So for the purpose of WoL the two ends of the Wireguard tunnel are in two different, not connected networks. In theory you might be able to make it work using subnet directed broadcasts - though creating some means to trigger the WoL packet on where you're terminating your Wireguard might be easier to manage.
Simple option would be just logging in via SSH to trigger it (you could script that - define a host in your SSH client config that just executes a command on connection), or something like a simple web frontend which will then trigger the WoL event.
¹ it is probably fair to assume nowadays that you're using Ethernet, and not something like Token Ring. In case you do it still works the same, just the terminology is different.
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.