I believe that ladder, and by extension TMM, are supposed to provide the canonical 1v1-4v4 experiences for FAF. Consisting of maps that provide the 'correct' style of gameplay and put the type of skills a player is 'supposed to have' to the test. External factors, like the fact that some people play a map a lot in custom games, or some mapper wants to force people to test their map, should not be given any consideration. Setons is the ultimate canonical 4v4 map that tests pretty much all the 4v4 skills players should have, so it obviously should be a potential pick for map pools.
If you instead view matchmakers more casually, as a replacement for custom games, then Setons should still be in the pool. It would be pathetic and defeatist to exclude the maps people play in custom games from matchmakers. Then you are forcing players into custom games if they want to experience Setons, the most canonical FAF experience. The reason other popular maps, like gap and astro, should be excluded from matchmaking is that the gameplay they encourage is not 'proper' according to FAF culture. They are not excluded just because they are popular in custom games.