The point was that if the extra (light) ballast is at the lowest point of the ship, the centre of gravity might well be compromised. Ballasting a model does not quite follow full size rules. As a rule, we don't carry variable cargo, a real ship does and so needs ballasting, and is designed with this in mind. A model, on the other hand, is built to work at a given weight, and if we park our batteries (the best ballast) too high we can run into problems.
Incautious building can create stability problems as well. I recall a case of an article in a mag several years ago. The guy had built a liner, very good-looking. He was mystified as to why it exhibited loll. The simple fact was that he had far too much weight in the superstructure - any more and he would have been re-enacting the Poseidon event. I would hold that in a model, you need your structural centre of gravity as low as possible, therefore any added water ballast should be above any "solid" ballast, or at least sited so as not to raise the centre of gravity.