Connecting to fly.io and fasterthanli.me (hosted by you) using IPv6 fails because PMTUD is broken. My client doesn’t receive TLS Server Hello response most of the time; when I manually set MTU = 1480 (and consequently the MSS option), the connection works. Sometimes (about 15 % of the time; I didn’t do any statistics here) things go well; I suspect this is the same/similar issue as described in IPv6 PMTUD issue.
Because I would like to have people in my house to be able to use sites hosted by you, I was forced to artificially lower the MTU of the WAN interface of my MikroTik router, causing inefficiency for everything else.
I uploaded a base64-encoded PCAP file demonstrating this issue: the first two connections failed, while the third succeeded. It was captured on the WAN ethernet interface of my MikroTik: you can see all the encapsulating headers (PPPoE, VLAN). This was captured with the MTU of the WAN interface set to 1500, MTU on my PC also equal to 1500.