along with the visual asymmetry of the ascent stage and decided that the CoG and thrust axis were deliberately misaligned. He totally disregards the fact that the CoG is a bit of a moving target, being affected by equipment stowage, crew movement, propellant usage, etc.
Yes, he totally disregards the entire science of spacecraft dynamic control. Where to begin...
First of all, the conceptual control axes for the LM were
not orthogonal, as was the case in the other spacecraft. This bias was intended to correct for the fact that the LM flew "forward" for a great deal of the landing. And nowadays we are perfectly happy with non-orthogonal control axes; we deliberately do not align reaction wheels along cardinal axes or in orthogonal planes precisely so that we can use a subset of them to maintain control after the failure of a wheel.
Second, no RCS design or control law, or indeed any accelerated-flight control law, requires the spacecraft to have "aligned" mass properties. Such a thing is impossible to achieve in practical design, and further impossible (if that concept means anything) to maintain in normal operation or powered flight. No method of flying a spacecraft has ever relied on delicately balancing the mass properties so as to require no imposed pointing control. Even the basic skyrockets from thousands of years ago required arranging the center of (aerodynamic) pressure to provide a corrective moment.
Third, the RCS system provides control
moments. The jets do not fire continuously during powered flight. The spacecraft, as all spacecraft do, wanders around its deadband until a control moment is required.
Fourth, on the ascent the RCS was operated in pulse mode because it was
too powerful for the largely empty spacecraft. It was sized to provide adequate control moments for the docked and fully-fueled spacecraft.