Quantum physics uses links; when making Quantum Gates, the particles that make up the 'Quantum' part must be created together, so that they are connected, and then they will be split to be taken to different gates. Changing channels to a different Gate would mean using different particles. Basically, that's just a link between the two. While the whole warp-to-different-dimension-and-back will effectively leave a trail to nothing, the Quantum Gates still operate in the same dimension, making them traceable.

Besides, I can't focus on just one empire, or those 1000 or so colonies will just be eaten up. The EA has become the target, now