I just investigated on Xenial, and this problem appears not to exist
there. The behaviour is the same (SYN+ACK retransmission after
TCP_DEFER_ACCEPT timeout), but this time nginx correctly continues the
connection. So it seems that this was fixed somewhere between trusty and
xenial.

For the fixed version:

  lsb_release -rd:
    Description:        Ubuntu 16.04.1 LTS
    Release:    16.04

  apt-cache policy nginx:
    nginx:
      Installed: 1.10.0-0ubuntu0.16.04.2
      Candidate: 1.10.0-0ubuntu0.16.04.2
      Version table:
     *** 1.10.0-0ubuntu0.16.04.2 500
            500 http://mirrors.digitalocean.com/ubuntu xenial-updates/main 
amd64 Packages
            500 http://mirrors.digitalocean.com/ubuntu xenial-updates/main i386 
Packages
            500 http://security.ubuntu.com/ubuntu xenial-security/main amd64 
Packages
            500 http://security.ubuntu.com/ubuntu xenial-security/main i386 
Packages
            100 /var/lib/dpkg/status
         1.9.15-0ubuntu1 500
            500 http://mirrors.digitalocean.com/ubuntu xenial/main amd64 
Packages
            500 http://mirrors.digitalocean.com/ubuntu xenial/main i386 Packages

In essence, this appears to have been fixed in between 1.10.0 and 1.4.6
of nginx.

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https://bugs.launchpad.net/bugs/1619687

Title:
  nginx incorrectly handles slow connection in deferred mode

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