Oh yeah. You are right. Those can affect the stats! However what I see from the stats. Usually when someone is really good with one faction they are also pretty good with other too
1v1s play entirely differently from every other game mode so its rare(some exceptions) you'll find primarily team game players transitioning to 1v1 and instantly being good at it. some factions also play entirely different, ex, USF playstyle is the polar opposite of Ostheer. while true to some extent (if you are top 200 as one faction you are better at others), Its not always the case.
All that being said, when analyzing statistics between games all the players involved should be top 200, while its rare team games meet this category the games that make it will be infinitely more valuable when basing balance decisions off of it.