Well, I only managed to replicate it on Ubuntu, and it requires many conditions 
to be met:
- 6in4 tunnel to HE.net
- ipv6 rules applied
- ipv6 forwarding enabled

Removing/replacing any one of these made downloading (wget -O /dev/null)
reliable for at least 3 repeats of a large (~1GB+) downloads.

I recreated the setup on Raspbian, and so far haven't had the issue.

** Summary changed:

- Raspberry Pi 3 network dies shortly after a burst of SD card IO and network 
load ((lan78xx): transmit queue 0 timed out)
+ Raspberry Pi 3 network dies shortly after a burst of IPv6 tunnel network load 
((lan78xx): transmit queue 0 timed out)

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

Title:
  Raspberry Pi 3 network dies shortly after a burst of IPv6 tunnel
  network load ((lan78xx): transmit queue 0 timed out)

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