Sorry for the delayed response. I moved my network back to RPi1 so I can
do experiments on the affected RPi3.

I'm thinking, if this is indeed caused by the usage of a 6in4 tunnel,
and you're unable to set up one with HE.net because of
unavailability/ISP restrictions, it should be possible to set up a 6in4
tunnel within your own network (obviously, another host would be needed
for this). I'll try to provide a config/script/whatever that would do
this.

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https://bugs.launchpad.net/bugs/1861936

Title:
  Raspberry Pi 3 network dies shortly after a burst of SD card IO and
  network load ((lan78xx): transmit queue 0 timed out)

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