As I tried to say in the description - the STL file is already scaled to fit V2 (the one with integrated dice tray). If you use V2 it should fit as is without scaling it up or down. You only have to scale it down to 96.71% if you want to use it for the original thing.
If you want to use the new top element from the original thing for V2 (the one with integrated dice tray) then you have to scale the new top element up to 103.4% to fit the rest of the V2 objects.
It may be a bit confusing - I hope that made it a bit clearer. What I did a lot to waste less filament and time while testing was to only print a few centimeters from top and bottom and deleted the rest of the tube with a plane cut in Meshmixer. Maybe you want to do the same to make sure the size is correct for your model.