Update 2026-03-07: Proton has added the IPv6 configurations mentioned below to the WireGuard config files that you can get through the web dashboard. The guide below is for historical purposes only.
The Linux app supports IPv6 over the VPN but still connects to the VPN server using IPv4.
It's possible to make changes to the WireGuard configs that you can get from https://account.protonvpn.com/downloads to enable IPv6.