You know, I took Snyder at his word regarding the trunks; he wanted them, and they tried to make it fit within the framework they were working with, re; the Kryptonian undersuit; but that doesn't make sense.
If it's already an "undersuit," over which they add other clothing elements, why NOT have a trunk like part?
First off, there are no "rules" for such a type of clothing, especially if YOU'RE the one constructing the story around the how and why of said clothes.
Second, if it's largely treated as an UNDERsuit, why not have an underwear type area?
Of course it's not JUST for going under the other clothing and armour elements, and is meant to function as "regular" clothing as well, but whatever.
Main point is, it's something they were designing from the ground up, not just the design, but the entire concept.
Bah, any who, long story short, I'm still quite happy with the final design, even though I didn't care for the \S/ design they went with; though it also made sense within the overall design aesthetic they were going for on Krypton, and looked perfectly good on screen.
That said, I don't see why they would NOT include the emblem on the cape. Clearly the house symbols are important in that culture, and so are the capes, why wouldn't they want to identify themselves coming and going?
Hell, considering the velvet like nature of the capes, I would have accepted a basic texture formed glyph on the cape. Kind of like what thy do with horse hair/fur, simply brushing over a stencil in the opposite direction of the flow of the rest of the hair.
Would have been a less ornate approach, and feel less like he's trying to push his brand or something.