“Monopole shift is always up” means: if you only spread the same nuclear charge over a finite volume (no extra charge added), the energy moves up.
Toy model A is different because it adds an extra negative charge inside the nucleus (without compensating elsewhere), which just makes the atom more bound, so the energy goes down.
So there is no contradiction: the “always positive” claim applies to finite-size at fixed total charge, not to changing the total charge.