That wouldn't matter too much as long as the sample size is large enough, because then on average every faction would have a roughly equal amount of games won due to skill gap. Sadly though we do not have access to up to date and complete automatch stats either.
Ideally we'd have access to big data (the game collecting information on literally everything) like most modern games, but CoH2 does not have that.
In the end, the best we can do is use (somewhat outdated) automatch and tournament stats as indicators (but as an indication only), while using our gut feeling along with talking to top players (because ultimately only at top level can we eliminate as much external influence, i.e. l2p issues, as possible) and keeping an eye on community sentiment to get a rough estimate of what the faction balance is currently like. Obviously not much of a scientific method, but I'd say it's been working well enough for the last 1.5 years.
Automatch always tries to match players with equal elo. That can mean rank 100 faction X vs rank 500 faction Y because they have the same elo rating due to either faction imbalance or lower player numbers in a ladder. That's why automatch stats are pretty much meaningless because they will always tend to be very close to 50% apart from maybe the top 1% of each ladder.