It's not just that. Imagine how it would weirden up the gameplay. The results of more than two teams are simpler in team battle or domination, whereas in CTF you'd lose the balance of "if we have their flag and they don't have ours, we can score". For example, if you're on the red team, you have the green flag and the blue team has your flag, can you score or not? If not, how difficult it would be to score if you have to keep your flag safe for scoring from two or three different teams? Or if yes, would people exploit it by attacking always the team that doesn't have your flag?