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What is the downside of using tailscale over wireguard?
I don't think there's any significant downsides. I suppose you are dependent on their infrastructure and uptime. If they ever go down, or for any reason stop offering their services, then you're out of luck. But yeah that's not significant.
The reason I want to do this is it gives me more control over the setup in case I ever wanted to customize it or the wireguard config, and also teaches me more in general, which will enable me to better debug.
AFAIK their infra is only used for configuring the VPN. The VPN itself is a regular peer-to-peer Wireguard VPN. If their infra goes down while a VPN tunnel is connected, the tunnel should keep working. I've never tested that, though.
You can self-host your own Headscale server to avoid using their infra.