Is the overhead of using protocol 41 smaller than encrypted vpn protocols?
http://packetpushers.net/ipsec-bandwidth-overhead-using-aes/
Therefore, am I correct to say that the overhead of protocol 41 is smaller because it is just putting IPv6 packets into a IPv4 packet without any handshaking with the protocol 41 peer?
I'd agree with that. P41 is 20 bytes overhead, whereas IPSec and options can eventually add up higher. Don't know about GRE, but its easy enough to research if you need to.
Do you know any similar mechanism which can be used for sending Layer 3 transparent packets with low overhead and no need handshaking over IPv4 internet?