Multi-WAN + Transparent Proxy doesn't currently work in FreeBSD.Cheers,Franco
On Windows you should be able to do this via a group policy - then you would have it inside most apps (except some which bring their own trust store) and on Linux you would have to use some kind of an automation tool which will copy the certificates on the system and updates the ca store. On Linux you can set the environment variable HTTP_PROXY inside a login script so the applications will be aware of an proxy if you are not using a transparent proxy.