Thrust limit penalty is applied when you account for wind anti ice on your performance.
My company uses airbus flysmart where you can select wing anti ice for takeoff or landing performance in the respective application.
Regarding the enroute consideration, there are 2 ways imho:
1) Just add the most restrictive choice (total A/I on). That would be the safer but not the optimum if it really messes up with your enroute driftdown terrain restrictions.
2) Add the additional weight penalty to your actual weight to find the driftdown altitude. E.g GW 70T. Penalty on single engine driftdown is -4200ft (OAT>15C) according to MEL. Calculate driftdown values for GW 65.8
Airbus flysmart in-flight app is a very easy EFB app to use if your company has it.