It's been multiple StrongSWAN updates since then and no additional info, but if the issue reappears, feel free to reopen.

Done some further research about rt_netlink and charon relationship. As described in the docs of Strongswan the option charon.process_route = no helps and is a good workaround if the destination is always reachable over a known specific interface (i think it can be an issue if wan load-balancing etc. is used).