How to scale up modernist Potato Puree?

Assuming it says 100% for the potatoes, I don't think you've got the scaling right. The recipe format picks a baseline ingredient, then gives the quantities for other ingredients as percentages of that ingredient. So if it says potatoes 100%, water 200%, then for 1kg of potatoes you need 2kg (2L) of water. See the detailed explanation from the source. The point here is to make things really easy, not to make you do awkward extra math.

As for the bags, you should definitely use two bags. If you do have two identical bags the size of the original one, your circulator is still keeping the water at the right temperature, and you've put in more water as directed by the recipe, it should take close to the original time. If you put it all in one bag, it'll take longer, and exactly how much longer is pretty hard to guess, since it depends on exactly how you pack it into the bag.

I think the issue you're referring to is that more potatoes require more time to cook to the consistency achieved by following the original recipe.

This of course (like many other cooking issues) is a thermo dynamics problem. As long as you make sure your potato pieces are small enough (I make about 1" think slices) then add twice as much water (that's what they mean by 200%, 1.5Kg of potatoes -> 3L water).

In a sous vide, it would be better to have two bags separate as opposed to one big one. The name of the game is to allow the heat to penetrate. The rate of cooking something twice as thick is not twice as long (it follows heat diffusion formula). By separating the bags you allow the circulator to replenish the warm bath around the food.