You have not produced a single argument why the "top 200" are better instead there is an indication that the number might be inflated for some faction due to lower player count. There has even been a thought that one should use % of the top player instead of rank 200 to reduce that effect.
On the other hand from the stat it already clear that a low number of games result in different stat.
If top player matter more than number of games than stat should be of the TOP 10 player only.
The fact that in some games their might be some player of lower level in all mode and factions does not mean anything unless:
you know in how many games that happened and the number is significant
or
some how provide indication the correlation between lower player and a specific faction improving the win rates of certain faction.
In sort do decided to use one set of stat over the other you need to find a convincing explanation of the difference in win rates.