Ng+% as we've thought it among ourselves was using a pre-existing save starting from the earliest quest in the story line, using whatever you think is best, Encore% as I think it should be is starting the game from the beginning and completing Ng and Ng+ with whatever is obtained during the run

In my runs that I've done so far I stopped the timer at the beginning of the city return cinematic (I haven't submitted any because I forget to split or I don't record) but I think its better to change the ending of any% to the city cinematic that plays upon returning to it. Also Encore% would be starting the game from the very beginning and beating it twice, to obtain the "true" ending.