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This could be the I/O overhead caused by docker while using NAT networking: https://stackoverflow.com/questions/21889053/what-is-the-runtime-performance-cost-of-a-docker-container#26149994
The article your linked is citing a paper from 2014. Seems hard the believe the network stack hasn't been significantly reworked in 10 years. That being said I don't have anything to refute this.
Does the above still apply if using a glutun VPN docker with other containers connecting directly to glutun?
That's a large penalty, wow.
It's huge for networking. VPN gateway (for accessing the VPN WAN over LAN) on the host is 20-40% faster than dockerized...
I'm using NAT for sure. All my containers are on a different subnet than the host.