Though your observations are correct, you'll find that certified aircraft are designed so as to minimize these affects. As Mark mentions, dihedral plays a role in this. There is nor requirement for determination or control of the vertical position of the C of G. Even, a Lake Amphibian, with the engine way up there, does not really show much affect in this regard.
You can see the affect of vertical C of G when amphibious floats are installed on a wheel plane. There is a noticeable pendulum affect in some float planes, as the C of G is much lower. While a passenger once in a C 185 amphib, I asked my friend the owner/pilot, if the pendulum affect was so great, as to prevent the aircraft from being rolled. A minute later, we had the answer - a 185 amphib can be rolled!
The installation of a STOL kit leading edge cuff on a Cessna wing can have the affect of very slightly reducing the lateral stability, but because of the effective dihedral as seen at the leading edge, not the weight of the kit.