The center of mass thing would be a valid issue if they were producing conventional thrust. But they emit a "warp field" that's more akin to an EM transmission than to real thrust. Hence my antenna analogy from my previous post.
The star trek ships use their impulse engines to produce this real thrust. And while they are often comically small for what they do, to their credit they are often positioned in a way that should be aligned with the ship's center of mass.