Quite the opposite, actually.
Differences in skill levels and "l2p issues" should be much less impactful for top-rank players than they would be for the broad mass of players which would undoubtedly make up the vast minority of a random sampling.
Essentially, it comes down to whether or not you want to balance "from the top".
For balance purposes you absolutely should consider the top ~500 players more than anyone else. But when we're talking about overall faction win rates it's important to think about the other skill brackets too. Especially when we compare across game modes. I doubt there's very many pro teams playing 4v4, so perhaps the OKW inflated winrate is simply a matter of lower skill and not inherent imbalance.
IMO win/loss rates are very rarely indicative of actual balance issues. When I played DoW2 most factions had pretty even win/loss ratios, but player distribution between factions was heavily skewed. And it didn't really have much bearing on the actual game balance, since for the entire lifetime faction win/loss was similar despite huge imbalances. (Because again, pro players can make anything work by simply outplaying lesser opponents often enough to inflate their ratio.)