Fair enough but i am not sure how big this issue actually is.This is indeed a major problem because every tournament nowadays bases its seeding, at least in part, on the 1v1 DE ladder.
Which means you could potentially have a player with a very inflated rating (due to playing just 1 map) taking the spot of a much better player.
Just think of this, there was a time where the highest rated player on Voobly was a guy who played exclusively 1v1 Michi DM...
You are right it will be less accurate but i think there are plenty of ways to work around this especially with everyone in the top being very known in our small community. Rating has never been the perfect metric for skill and a lot of the seeding is done based on past performances aswell. We might get some exceptions ofc but id argue we already have those a lot anyways with people playing one map or civ regardless.
I simply do not think it would weigh up against the pro's. And even if we get some huge exceptions people will know about it since the top rated community is very small.
And there is plenty of other stuff to think off, force people to play 10 ara games for example before they can sign up for an ara tournament or accept a 100elo penalty for your elo.