Test image: libreelec-rpi2.arm-9.0-set-tos-ntp.img.gz
After it boots set tos with command below and reboot. Then time should be set with NTP.
cat > /storage/.config/system.d/ntp-set-tos.service <<EOF
[Unit]
Description=Iptables set TOS for NTP
Before=network.target
Wants=network.target
[Service]
Type=oneshot
ExecStart=/usr/sbin/iptables -w -t mangle -I POSTROUTING 1 -p udp --dport 123 -j TOS --set-tos 0x00
ExecReload=/usr/sbin/iptables -w -t mangle -I POSTROUTING 1 -p udp --dport 123 -j TOS --set-tos 0x00
RemainAfterExit=yes
[Install]
WantedBy=multi-user.target
EOF
systemctl enable ntp-set-tos
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Would be probably easier to patch connman to use TOS 0x00. Or run patched ntpd from http://autostart.sh/custom service. Or use curl approach.
Update: Seems there were at least one user with same problem Raspberry Pi 3 built-in WiFi SSH NTP Problem