Reading it again with fresh eyes, it's more than 44km but they're still ranked 6th and 7th overall for distance covered. Yes this only counts the factory cars and not AF Corse #83. Penske beats Ferrari AF at 6 circuits to Ferrari's 4, whilst they've both completed 965 laps in Bahrain.

I am considering them as separate yes. I haven't split Audi Sport Team Joest and North America, but have tracked the two Alpine Hypercar eras individually, everyone else falls under one name. Porsche Penske should be the next team to reach 50k km funnily, as they're currently 44km ahead of Ferrari.