Assume you have a 3-cap:
You need to leave FR and go mid. Why? Because your enemy can't breach MT, can't breach BET, and can't breach mid. Why defend a base that's inaccessible to the enemy anyway when you could gain a huge positional advantage against the enemy team? If a rogue takes it, it's one rogue. Go kill the !@#$ and get on with your game.
Can't seem to get a 3-cap? Leave defense at your two bases, get heals in mid and get the flag. If there is an incoming to a base, call your healers.
If you say "3 bases > flag" at the start of every EotS game, it's actually because you suck and you want to imitate other players who you think know what they're talking about when they also mindlessly start every EotS game with that same mantra.