Matt,
WOW, you get the record for the longest post! No problem though, I enjoy the challenge and respect your concerns to get this right. My first thought when reading your post was these are pretty large windows and are going to be used in a formal setting (living and dining rooms) why not go to a 2" wood pole. My opinion about 1 3/8" Wood is it is very small. Drapery hardware should really help show off your beautiful drapes. Yes, 2" does cost more but the change in the look is dramatic.
Here are the answers to your questions:
1. If you have mahogany furniture in the room it will look good using mahogany hardware for the curtains. You could go to the color "Anodized Bronze" but I prefer to see more of a contrast between the panels and hardware to make everything pop out.
2. The master bedroom is a tough one. You want to use wood hardware in this but Kirsch does not make a double wood bracket. The best way to tackle this window, since the sheers and curtains are the same height is to use a double wood bracket (from another vendor, which we have) or attach a inside mount wood socket to the 6" projection brackets. This way you will have every thing the same height. If you need me to explain the bracket thing to you in more detail just give me a call. For this to work you will definitely needs to use a 2" diameter wood pole to go the 6 foot span between brackets. 1 3/8" will flex in the middle if it goes more than 5 feet. Your decorator suggested using the travers rod in the back and I am not fond of that idea. Here is why! I like continuity when using hardware. The white traverse rod will be visible at all times behind the wood poles. If this does not bother you than it is not an issue. It is just something that I view as a quick fix and won't have your best interests.
3. The rod size I addressed above. Each size will look good since Kirsch make a good product. I am just partial to the larger diameters.
On another note, have you had an chance to look at the LJB wood hardware we have on our site? This is very similar to the Kirsch but the cost is significantly less. It is all hand finished here in the us (Kirsch is finished in China) and is very high quality. It might be worth taking a look. You could possibly get the 2" from LJB for the same price as the 1 3/8" from Kirsch. Here is a link.
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I hope this answers most of your questions. You can always call me or just respond to the post.
Dave