They are not directly comparable. Nebula is a mesh VPN. Wireguard can be used as a building block for a mesh VPN (as it is in Tailscale), but it does not have that function organically.
I have tried Tailscale / Headscale and did not find the overhead worth it. Both can saturate a 10Gbps link and that's all I need right now. Nebula's much simpler to administer. The configuration's spelled out in the client configs and in the certificates you provision. If you're already using some form of configuration management, it's quite easy to make changes. If you require a Web UI, Tailscale / Zerotier / etc may be better. There is a company that provides a Nebula-based service with a Web UI but I haven't tried it.
I'd characterize it as such: Wireguard is more of a plumbing solution that gives you a point-to-point connection, either it's enough for you or you can use this to build what you need.
Nebula is more of an end-user ready-to-use solution, gives you features like NAT traversal, automatic selection of direction connections if possible, the nodes don't need to know other nodes' addresses ahead of time(x) etc.
Looking at that file may make you reach misleading conclusions. Some tun/io code may be use but there's that. As far as I understand WireGuard the protocol is not used anywhere:
nebula (master)> git rev-parse HEAD
2b427a7e8934f0a436fea25eb40a6b979b34ee7a
nebula (master)> rg --glob '*.go' -i wireguard
wintun/tun.go
6: * Copyright (C) 2018-2021 WireGuard LLC. All Rights Reserved.
9://NOTE: This file was forked from https://git.zx2c4.com/wireguard-go/tree/tun/tun_windows.go?id=851efb1bb65555e0f765a3361c8eb5ac47435b19
udp/udp_rio_windows.go
4:// Inspired by https://git.zx2c4.com/wireguard-go/tree/conn/bind_windows.go
25: "golang.zx2c4.com/wireguard/conn/winrio"
overlay/tun_wintun_windows.go
17: "golang.zx2c4.com/wireguard/windows/tunnel/winipcfg"
wintun/device.go
6: * Copyright (C) 2017-2021 WireGuard LLC. All Rights Reserved.
9://NOTE: this file was forked from https://git.zx2c4.com/wireguard-go/tree/tun/tun.go?id=851efb1bb65555e0f765a3361c8eb5ac47435b19