I successfully managed to get Linux VTI (Virtual Tunnel Interface) working with strongSwan. By using VTI it is no longer needed to rely on the routing policy database, making understanding and maintaining routes easier. Also with VTI you can see the cleartext traffic on the VTI interface itself. It was confusing to see actual tunnel traffic before using tcpdump using the standard policy database setup. (There are ulog/nflog hacks to see cleartext traffic in both direction though, similar to BSD pflog.)

With policy database strongSwan installs its learned policy routes to a separate routing table having preference over the main routing table. strongSwan does not support native VTI setup so a <left|right>updown script is needed to setup the tunnel this way.

So far the /usr/local/sbin/ipsec-notify.sh file looks like this:

#!/bin/bash

set -o nounset
set -o errexit

VTI_IF="vti${PLUTO_UNIQUEID}"

case "${PLUTO_VERB}" in
    up-client)
        ip tunnel add "${VTI_IF}" mode vti \
			local "${PLUTO_ME}" remote "${PLUTO_PEER}" \
            okey "${PLUTO_MARK_OUT%%/*}" ikey "${PLUTO_MARK_IN%%/*}"
        ip link set "${VTI_IF}" up
        ip addr add ${PLUTO_MY_SOURCEIP} dev "${VTI_IF}"
        ip route add <tunneled-network> dev "${VTI_IF}"
        sysctl -w "net.ipv4.conf.${VTI_IF}.disable_policy=1"
        ;;
    down-client)
        ip tunnel del "${VTI_IF}"
        ;;
esac

and the relevant part of /etc/ipsec.conf looks like this (without authentication method details):

conn <vpngw>
    leftupdown=/usr/local/sbin/ipsec-notify.sh
    left=%defaultroute
    leftsourceip=%config4,%config6
    rightsubnet=0.0.0.0/0,::/0
    right=<vpngw_ip>
    rightid=<vpngw_id>
    auto=route
    mark=2

In /etc/strongswan.d/charon.conf uncomment install_routes and install_virtual_ip properties and change their value to no:

# Install routes into a separate routing table for established IPSec tunnels.
install_routes = no

# Install virtual IP addresses.
install_virtual_ip = no

Update #

Thermi has turned this blog post and other related informations into a strongSwan wiki entry. Please be sure to check that out too.