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Does this mean, that NICs computes checksums inside vxlan payload? As far as I understand, the major additional cost of vxlan comes from additional passing thought the whole network stack, which includes iptables and routing.

Yes, you're right. We have to edit article's introduction.

Our original intention in doing this research is to answer the question "how much do we lose in terms of latency and throughput?" So, as you've said, flannel's aws-vpc is equivalent to out of the box k8s/AWS solution, flannel's host-gw is equivalent to calico. Since they use same "backend", in benchmarks we focused on flannel because it's easier to switch in flannel from one configuration to another (basically just put new config via etcdctl and restart the daemons).

However, thanks in pointing it out. In the article we should state our motivation clearer and add references to another solutions, such as calico.

Calico looks good. As far as we understand calico works the same way as flannel/host-gw does, i.e. creates a route for all subnets in the cluster. Of course, calico is more advanced technology than flannel/host-gw, but the reason why we haven't tested it is following: they're different in control path but the same in data path. Our original intention was to test underlying linux-kernel mechanisms and understood how much we lose in terms of latency and throughput.

For small configurations flannel/host-gw is OK, I guess, but if one have several kubernetes clusters, flannel/host-gw becomes harder to maintain. That's a place where calico should be useful.

Yeah, Joyent's VLANs looks very interesting but as far as I understand I can't deploy it amazon ec2, since I need special hardware for it. Am I right?