voici pour ceux que ça intéresserait le script qui fait la config de bout en bout
Il est à lancer avec le scheduler au boot.
3 variables à modifier, le nom de l'interface physique du mikrotik utilisé pour connecter l'ONU, l'enregistrement de l'entrée DNS personnalisée sur le portail de Free et l'adresse MAC de votre Freebox. Ca fonctionne pour moi, je suis curieux de vérifier la portabilité.

#Modify the interface name where you connect your ONU & the name on CustomDNSFree
:local interfacePhysical "sfp1"
:local CustomDNSFree "xxxxx.hd.free.fr"
:local MACFree "FF:CC:EE:4B:2B:3A"

:local interfaceInternet "vlan836-free"
:local ipipv6 "ipipv6-free"
:local ipv4Free "ipv4-free"

delay 10s
#add interface list WAN
:if ([/interface list print count-only where name="WAN"]=0) do={
/interface list add name=WAN
}
#Cleanup list member orphans
/interface list member remove [find where interface~"^\\*[0-9a-fA-F]{1,8}\$"]
#add vlan 836
:if ([/interface print count-only where name=$interfaceInternet]=0) do={
  /interface ethernet set $interfacePhysical l2mtu=1796 mtu=1704 mac-address=$MACFree
/interface vlan add name=$interfaceInternet vlan-id=836 mtu=1700 interface=$interfacePhysical
/interface list member add interface=$interfaceInternet list=WAN
}
#add ipv6 address for ipipv6 tunnel
:if ([/ipv6 address print count-only where comment="interfaceInternet2"]=0) do={
/ipv6 address add address="fd99::0ffff/128" interface="$interfaceInternet" advertise=no comment="interfaceInternet2"
}
#add FW rule
:if ([ :len [/ipv6/firewall/filter/find where comment="Allow IPIPv6 tunnel on WAN" ]] = 0) do={
  /ipv6 firewall filter add action=accept chain=input comment="Allow IPIPv6 tunnel on WAN" in-interface-list=WAN \
protocol=ipencap  place-before=*0
}
:if ([ :len [/ipv6/firewall/filter/find where comment="Allow dhcpv6 replies on WAN" ]] = 0) do={
  /ipv6 firewall filter add action=accept chain=input comment="Allow dhcpv6 replies on WAN" dst-port=546 \
in-interface-list=WAN log=yes log-prefix="fw, a: allow6, r: aid, " protocol=udp src-address=fe80::/10 place-before=*0
}
#add ipv6 DHCP Client
:if ([/ipv6 dhcp-client print count-only where comment="fibre-free"]=0) do={
/ipv6 dhcp-client
add comment="fibre-free" interface=$interfaceInternet pool-name="pool-freeV6" pool-prefix-length=60 request=address,prefix script="#Modify the \
    CustomDNSFree\r\
    \n:local CustomDNSFree \"$CustomDNSFree\"\r\
    \n\r\
    \n:local interfaceInternet \"$interfaceInternet\"\r\
  \n:local ipipv6 \"$ipipv6\"\r\
    \n\r\
    \n:local prefix [/ipv6 dhcp-client get [find interface=\$interfaceInternet] value-name=prefix]\r\
    \n:set prefix ([:pick \$prefix 0 ([:find \$prefix \",\"]-3)])\r\
    \n:local gw [/ipv6 dhcp-client get [find interface=\$interfaceInternet] value-name=address]\r\
    \n:set gw ([:pick \$gw 0 ([:find \$gw \",\"])])\r\
    \n:local addresse0ffff (([:pick \$prefix 0 ( [ :len \$prefix ] -1 )]) . \"0:ffff:ffff:0\")\r\
    \n:local prefix2 (([:pick \$prefix 0 ( [ :len \$prefix ] -3 )]) . \"2::\")\r\
    \n\r\
    \n#remove the uggly IP\r\
    \n/ipv6 address remove [find address=\"\$gw/128\"]\r\
    \n#set ipv6 for forwarding ipipv6 tunnel\r\
    \n/ipv6 address set [find comment=\"interfaceInternet2\"] address=\"\$addresse0ffff/128\" interface=\"\$interfaceInternet\" adver\
    tise=no\r\
    \n#set ip to the ipipv6 tunnel\r\
    \n/interface ipipv6 set \$ipipv6 local-address=\$addresse0ffff\r\
    \n#set IPV4 Free\r\
    \n:local ipv4free [:resolve \$CustomDNSFree]\r\
    \n/ip address set [find comment=\"ipv4-free\"] address=\$ipv4free network=\$ipv4free interface=\$ipipv6\r\
    \n" use-interface-duid=yes use-peer-dns=no

} else {
/ipv6 dhcp-client set [find comment="fibre-free"] interface=$interfaceInternet
}
#add ipipV6 tunnel
:if ([/interface print count-only where name=$ipipv6]=0) do={
/interface ipipv6 add name=$ipipv6 remote-address=2a01:e00:29:200a::fffd local-address=fe80::1234 mtu=1500
  /interface list member add interface=$ipipv6 list=WAN
}
#add ipv4 on ipipv6 interface
:if ([/ip address print count-only where comment=$ipv4Free]=0) do={
/ip address add address=1.2.3.4 network=1.2.3.4 comment=$ipv4Free interface=$ipipv6
}
#add route ipv4 on ipipv6 interface
:if ([/ip route print count-only where comment=$ipipv6]=0) do={
/ip route add dst-address=0.0.0.0/0 gateway=$ipipv6 comment=$ipipv6
} else {
  /ip route set [find comment=$ipipv6] gateway=$ipipv6
}
#
/ipv6 dhcp-client release [find comment="fibre-free"]