Lens of certain death and Lens of the killer are bypassing PvP protection as of ActuallyAdditions-1.10.2-r70.jar .
Also, I can't find an configuration to disable players interaction, nor disable Lens of certain death recipe.

Well.. the Lens isn't PvP, so there's nothing to bypass there.

But yes, the Crafting Option is indeed not present.

The Lens do kill other players, hence it's PvP.

But it's a machine not a player which kills

No, I consider PvP a player actively killing another player, that's why it's called "Player versus Player".
To me, your theory would also mean that lava is PvP. Sorry, but I don't think the lenses should be affected by any PvP option.

Players are very imaginative when it comes to bypassing PvP protection.
A laser can be placed by players to kill them inside a protected area, for example spawn.
Lava won't do that.

I don't care. I don't consider it PvP, so I won't change it.
Sorry, it's just my opinion.

That's your mod, I'm just telling you this part of your mod will remain disabled on most servers.