even the slightest variation in warp speed is millions of meters per second different
So what? If starships can go that fast, other technologies can probably go even faster. We know that communications zip across the galaxy quickly enough: a "radar" system based on these fast-moving information packets is all that is needed to track the enemy, even across a great speed differential.
Numbers, even big ones, are just numbers. There is absolutely nothing to suggest that megameters per second would be a major challenge, technologically speaking.