By the way, in this picture we can see that Van Gogh is wearing Lugnut's hearing device and drawing the portrait of Nefarious. I'm 100% sure it was some puzzle (like: Drew needs a picture of Nefarious for something, but since Van Gogh has problems with hearing, he'll draw it only in exchange for a hearing device. So Drew has to steal it from Lugnut).
Well flux is gone so nefarious could have him. Also note there is no bag. Maybe flux has that too. Please refer to the story development section to my theory about van goughs pencil, i think it would fit in nicely.
I think the bottomless bag is still here, it's just not shown during the dialogues and cutscenes. It would be very problematic to play without an inventory, even for some time (we don't have the bag at the very beginning of Toonstruck, but there are no real puzzles as well).