hi @Dmitry,
Noticed you are major contributor to accel-ppp 
Has the latest rolling release of VyOS got the latest version of accel-ppp? I checked their versions and they seem to match (1.12.0-95) but they have different build numbers.
PS; didnt get a chance to test L2TP with those IP tables changes you mentioned, the client has been mostly transition to SSTP. I’ll see if I can do some testing myself.