L2tp over IPsec is not working in VyOS 1.2.0 without configured NAT.
I've created the topic about this issue on VyOS forum and didn't get any replies.
Also I've found another topic about this bug with no replies.
Looks like the problem is in unique XFRM marking.
Without "mark=%unique" in ipsec configuration everything working fine.
More details are provided in the topics above.