Ross, it doesn't sound like you're actually disagreeing with what's been said. I don't think anybody's arguing that Ang Lee went into the wardrobe room himself and rummaged around on the racks finding the outfits he wanted.
But it sounds like, from what you said, it's quite possible for him to say, "I'd like these three characters to wear blue" to the costume designer. And then the costume designer came up with the specific items of blue apparel.
Both little Ennis in the flashback scene and Mrs. Twist are both wearing solid blue over tan plaid -- a combination that echoes the shirts in the closet. It's fairly unusual for a woman to wear a sweater over a shirt over a dress. When, on top of that, they aren't just any old sweater and shirt but ones in the colors of the men's significant shirts, it doesn't seem accidental.
Here again, it's possible that the costume designer came up with that brilliant idea him/herself, just as Heath Ledger reportedly came up with the idea of switching the positions of the shirts. But seems likely that the idea came out of discussions between the director and costume designer.