I'm guessing your mid-layer problem is envisioning HOW to use a mid-layer with your "everyday" button-down shirt. It is a little easier to layer OVER a worn base layer (a L/S or S/S wool or synthetic t-shirt) than removing your Sahara shirt to put another layer UNDER it. I have a similar MH Canyon shirt, but I almost never wear it and one reason is ease of layering. I don't have a good answer to this one; maybe someone should post a direct question about layering with a button-up "travel" or "hiking" shirt. I'm guessing folks just put take off their shirt and put a L/S base layer under it.
I think your list should look more like this:
*Base (choose 1, for hiking in):
REI Sahara Tech l/s shirt:
Smartwool lightweight l/s crew: 7.4oz
A L/S synthetic crew or zip-top: +/- 5oz
*Synthetic mid (choose 1, for hiking in if chilled):
Smartwool midweight l/s crew: 7.8oz
Patagonia R1: 10.1oz
*Down puffy layer (choose 1, for long breaks and in-camp):
Montbell UL Down Inner jacket: 6.4oz
Patagonia Down Sweater: 11.4oz
*Rain shell top (choose 1):
Tyvek suit: 6oz
DriDucks jacket: 5-6oz
UL WPB jacket: 6-12oz
Patagonia Houdini or comparable: 4oz
You want to build a modular clothing system with little redundancy (although there might be some) that will keep you (a) warm without overheating while you are walking and it is not raining, and (b) warm and as-dry-as-you-can when it is raining until you can walk out of the weather or make camp and change into dry and insulating clothing or a sleeping bag & shelter.
My base layer is usually a S/S wool t-shirt. I might instead wear a L/S wool t-shirt or a L/S or S/S synthetic t-shirt, all depending on the expected temps + humidity.
My mid-layer is a L/S wool hoodie or a Power Stretch L/S zip top, worn if I'm actually chilled while walking, otherwise in the pack. This base + mid would keep me warm enough at least into the low 40s/high 30s while walking, especially with hat + gloves + wind shirt.
My wind shell is a pertex hooded shell, that goes on when I stop or if there's, well, wind. If I'm not wearing it, it is in an outside pack pocket. Regardless of which wind shell you have (see David Chenault's recent article), they will ALL be more breathable than a WPB-laminate shell but still block any heat-sapping wind! A good wind shell works as part of a system that ALSO includes a rain jacket. My rain shell is around 6 oz and my wind shell is 4 oz. You are right, however, that one shell can do the job of both. In my opinion, this is just a case where two UL shells are better than one heavier WPB rain jacket.
My insulation jacket is a Montbell UL Down Parka or a MH Phantom (shoulder season) that I'm only going to be wearing on an extended break or in camp. I wouldn't hike in it unless it was below freezing and I was trying to get out of some bad situation.
Finally, a few other points:
You call this is a 3-Season list, but write about walking in below-freezing temps. You should probably adjust your list if you will be in extended below-freezing weather. I do think your Smartwool mid-weight layer or your R1 under your Sahara shirt would be fine while you are generating heat.
I don't think anybody walks through an afternoon thunderstorm comfortably, it's just a question of whether you are going to get eventually wet from condensation from your body or from the rain. If it doesn't last long or you stop for shelter, well, that's different.