The ECS Philadelphia still could have stumbled across Omega IV - in the latter years of a war that has lasted for almost a millennium - and not a stitch of canon would have been violated.
And I hate to keep bringing this up, but there really is no other explanation for how long those artifacts could have survived for over a thousand years, AND somehow turned up on an alien world. We all know they were originally created on Earth, after all. It's a matter of history, that everyone knows (or should know). And it's inconceivable that they could have arisen in identical forms somewhere else, thousands of years ago, with absolutely no connection with Earth! The laws of probability simply would not allow it.