I'm not using AAISP, but I have a very similar use-case and I'm not seeing marked packets on the l2tp interface. I'm pretty sure they're only put there once you add an mwan3 rule involving that interface. Just having mwan3 active won't add the marks unless there's a rule somewhere involving that interface.
I'm also on Virgin Media. It also irritates me they don't have ipv6. I'm however rolling my own ipv6 tunnel: I have a server in a datacentre and I've setup an l2tpv3 tunnel from my OpenWRT to my server in the datacentre, where my provider has delegated me a ipv6 prefix that I'm giving to my LAN for native ipv6 connectivity.
Like you, I use mwan3 to manage my two internet connections (in failover mode, not in load balancing mode).
I don't have any mwan3 config involving the l2tp interface. It's not routing any ipv4. So it doesn't need any mwan3 rules. Anything ipv6 goes in and out over that interface since it's the only ipv6-enabled interface on my router.
I put some catch all logging rules into my PREROUTING table to look at the traffic on that interface and literally nothing is marked. Two examples below - I SSHed over ipv6 to my server and I pinged one of its ipv6 interfaces.
Below is what it logs and it's notable for the absence of any firewall mark.
I haven't got the l2tp interface defined anywhere in mwan3 and neither do I have any mwan3 rules.
I suspect that defining the interface in mwan3 (or adding an mwan3 rule involving that interface) causes packets to be marked.
So you can fix the problem by excluding that interface from your mwan3 configuration. If you only care about the ipv6 connectivity, then this is probably the way to go.
I imagine you don't care about ipv4 connectivity via AAISP anyway, since why would you choose to tunnel an ipv4 connection if you don't have to.
Mar 23 14:30:47 openwrt kernel: 4,522967,1550640558975,-;IN=l2tpeth0 OUT= MAC=aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa SRC=xxxx:xxxx:xxxx:xxxx:xxxx:xxxx:xxxx:xxxx DST=yyyy:yyyy:yyyy:yyyy:yyyy:yyyy:yyyy:yyyy LEN=80 TC=0 HOPLIMIT=64 FLOWLBL=517643 PROTO=TCP SPT=22 DPT=58462 WINDOW=64704 RES=0x00 ACK SYN URGP=0
Mar 23 14:34:49 openwrt kernel: 4,523296,1550882454085,-;IN=l2tpeth0 OUT= MAC=aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa:aa SRC=xxxx:xxxx:xxxx:xxxx:xxxx:xxxx:xxxx:xxxx DST=yyyy:yyyy:yyyy:yyyy:yyyy:yyyy:yyyy:yyyy LEN=104 TC=0 HOPLIMIT=64 FLOWLBL=294880 PROTO=ICMPv6 TYPE=129 CODE=0 ID=2 SEQ=1
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