Comment by dgl

This.

Instead you can create multiple Wireguard interfaces and use policy routing / ECMP / BGP / all the layer 3 tricks, that way you can achieve similar things to what vxlan could give you but at layer 3.

There's a performance benefit to doing it this way too, in some testing I found the wireguard interface can be a bottleneck (there's various offload and multiple core support in Linux, but it still has some overhead).