1) Pretty heavily leaning toward a walnut body. If I am wanting an 8-8.5 lb. bass am I going to necessarily need to get it chambered? Is this what Fodera refers to as "semi-hollow" on their price sheet? Any reason to think differently on the body wood? I see so many great comments here re: walnut.
As others have said: yes, you will likely need it chambered. I don't see any reason to think differently on the body wood. Walnut is an excellent option and Fodera is very experienced at working with it. They know how to bring out its best features.
2) I had been thinking I would surely go with the PJ setup, but the dual coils in the standard are really amazing. I feel like the preamp is designed to really complement the dual coils and they are unique to Fodera. That said, I have always loved the P-bass vibe. I do like that the dual coils can be run in passive mode if needed whereas I believe the EMGs are active only. Thoughts?
I like dual coils, but this is a very personal thing. Since you "have always loved the P-bass vibe" then you should probably go P/J.
3) I am great with having an abundance of articulation and love that about the standard model I have (pao ferro/3-piece maple neck/alder body/walnut top). So, ebony seems like a fine choice. But, I am really heavily leaning toward a Brazilian rosewood fingerboard. I love rosewood and nice natural mids. I mostly play fingerstyle. I am impressed with the 3-piece maple neck on my standard, so fine with that, but curious on thoughts re: going to 5-piece (Wenge streamers? Will they matter to the sound or not enough to care what the streamer wood is?) or even considering the white oak?
Fodera's upcharge for a Brazilian Rosewood fingerboard is frankly absurd. Brazilian Rosewood is a wonderful tonewood and indeed scarce, but it's not the only wonderful tonewood and it's not so scarce to justify the upcharge. I would go Ebony. Its durability makes a stellar fingerboard wood and its simple black color is a great way to accent a highly figured top wood. My background is in double bass so I may be biased toward Ebony because of that lol
The neck stringers aren't for sound so much as stability and aesthetics.
4) Top wood: Leaning toward something like a flamed koa or amboyna burl...I like the reddish hues. Any other wood types I should look at?
Perhaps a burled or flamed Redwood? Some Cocobolo has a lot of reds as well. And if you like a lighter red, a Pink Ivory might be nice. If they have a piece of Amboyna burl that speaks to you, though, I don't think you can go wrong there.
5) I definitely want a bit slimmer of a neck (at least at at the nut) as compared to my standard. I will have to take some measurements from my jazz bass as I really love that neck. And I want to go with mandolin frets (remember, I'm a fingerstyle player). I have mandolin frets on my jazz bass and dig 'em. I have grown into 40-95 pure blues strings on my standard, so see myself sticking to these strings going forward.
I don't see a question here. It sounds like you know what you want.
6) Other aesthetics: Probably go with pearl dot inlays and black hardware. I would love dark satin grey hardware, but doubt that's possible. I am thinking about rosewood pickup covers if going with the dual coil pickups. Large headstock? Does it matter? I would be fine to get a D-tuner, but probably would not use it much at all. Those that have it, is it annoying to have? Does it mess with the weight/balance of the instrument much?
Fodera is a custom shop so if you ask, they can probably order dark satin grey hardware for you. I feel like black will look best with the browns and reds of the woods you have mentioned, but it's your bass so get what you want

Definitely get wooden pickup covers if you go with the dual coins. It's a classy look and feels great if you rest your thumb on them. Rosewood will look good if you go with a Rosewood fingerboard; otherwise I'd match the top wood or go with Ebony to match the black hardware.
7) Oh, I'm planning to go with the dovetail neck joint. That seems like a good middle ground, though I like the idea of the neck-through as well. I probably slightly prefer the dovetail.
Again, this is a very personal choice. I like neck-though for the feel, construction, and sound, but a dovetail has the same feel and obviously works great as well.[/QUOTE]