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Why not? Thomas has won the race and finished second, and been an integral part in five other wins. Even if he doesn't focus on being a GC contender he's still a very valuable team-mate, and one who has shown many times before that he'll totally commit to the team.
Rowe is a rock solid team rider who also has supported multiple leaders in Tour winning teams and does a superb job of looking after a leader on multiple terrains.
Ineos' problem isn't with their rider roster, it's with their training regime and their day to day race tactics.
They won't quit but they won't (or shouldn't) be picked for the TdF again